Publications

Hansbro, P 2023, The Good Gut Anti-Inflammatory Diet Beat whole body inflammation and live longer, happier, healthier and younger, Pantera Press.
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Out of their mission to make people's lives better comes The Good Gut Anti-Inflammatory Diet. • Understand inflammation, a fundamental cause of many life-altering diseases, and the various factors causing it • Learn how balancing your ...

Hoppenrath, M, Murray, S, Chomerat, N, Horiguchi, T & Rhodes, L 2023, Marine Benthic Dinoflagellates - their relevance for science and society, 2, Senckenberg Kleine Reihe, Germany.
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This book is the most comprehensive summary of our knowledge of benthic dinoflagellate species, including a compilation of their toxins.Dinoflagellates are important primary producers, symbionts and, at the same time, heterotrophic consumers and parasites. The species composition in benthic habitats is quite distinct from planktonic habitats. Our understanding of benthic dinoflagellate biodiversity, biogeography, toxicology and ecology has improved but is still rudimentary. Benthic harmful algal blooms have attracted increasing interest because of the impact of ciguatera poisoning, the most important food-borne disease of non-bacterial origin worldwide, which is caused by benthic dinoflagellate species. Ciguatera poisoning appears to have increased worldwide in recent years. This publication is an updated summary of the taxonomy of currently described taxa and includes morphological and for the first time molecular genetic information for species identification. It contains the most comprehensive review of benthic dinoflagellate toxins published so far. The book also describes methods of study, discusses phylogenetics and evolution, and highlights their scientific relevance as well as the health and economic impacts of benthic dinoflagellates for society.Compared to the first edition (KSR Vol. 54), 64 new species, 20 new genera and 19 new combinations are described. All chapters have been revised to reflect the latest knowledge and more than 150 new publications have been integrated. The methods section has been expanded to include light microscopy, molecular genetic methods for detection and quantification, and toxicity tests and toxin analyses. For example, a new sampling method that can also be used for quantification is described, as is the metabarcoding approach to biodiversity detection. Species descriptions have been expanded, in many cases with information on molecular identification. The chapter on toxins has been updated. The chapter Rel...

Mahmud, MAP, Farjana, SH, Lang, C & Huda, N 2023, Green Energy, Elsevier.
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Green Energy: A Sustainable Future looks at life cycle assessment theory, practice, and methodologies applied in renewable energy power plants. The state-of-the-art life cycle assessment methodologies applied in power generation units are discussed following LCA analysis and key findings from energy production processes. Providing fundamental knowledge of how to measure sustainability metrics using life cycle assessment in renewable power plants, this title outlines state-of-the-art research about LCA methodologies related to low-carbon energy systems, their outcome, and how to relate the sustainable power concept with a circular economy. With theoretical concepts of LCA applied in low-carbon power generation systems, outlining environmental impacts based on comprehensive examples and case studies in solar PV, solar thermal, hydropower plants and micro-grids, this book is of great interest to engineers, policy makers, researchers and academics in the area of electric power engineering.

Alonzo, M & Fu, S 2023, 'Cocaine' in Encyclopedia of Forensic Sciences, Third Edition, Elsevier, pp. 573-585.
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Alonzo, M & Fu, S 2023, 'Hallucinogens' in Encyclopedia of Forensic Sciences, Third Edition, Elsevier, pp. 107-121.
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Alonzo, M & Fu, S 2023, 'New Psychoactive Substances' in Encyclopedia of Forensic Sciences, Third Edition, Elsevier, pp. 660-681.
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Falkenberg, LJ & Dupont, S 2023, 'Climate change and the ocean' in Oceans and Human Health, Elsevier, UK, pp. 265-288.
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The Earth's atmosphere is increasingly modified by human activities that are driving directional, sustained, and rapid global change. There will be a cascade of impacts on marine systems including sea level rise, storm events, ocean acidification, changes in salinity (primarily ocean freshening), and ocean warming and marine heatwaves. These global-scale changes will combine to impact human physical and mental health via changes to, for example, coastal ecosystems, infrastructure, and resources (e.g., freshwater supplies, food security and safety, medical compounds); disease transmission via mosquito-borne diseases, naturalized organisms, fecal-oral pathways; extreme conditions such as rainfall, storm surges, and flooding; pollutants, including in the air; and human displacement and migration. The impact of these global changes will depend on the local climate, nonclimate environmental conditions, and socioeconomic contexts in which they manifest. Understanding these complexities is central to managing our ocean so that we ensure human health under a future climate.

Frick, AA, Spindler, X & Bleay, SM 2023, 'Chemistry of Fingerprint Residue' in Encyclopedia of Forensic Sciences, Third Edition, Elsevier, The Netherlands, pp. 521-529.
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The chemical composition of fingerprint residue is complex and highly variable. Several components are susceptible to chemical modifications following deposition, which can have a significant impact on fingerprint recovery. In more recent years, interest has increased significantly in the information that can be gained from the chemical constituents of latent fingerprints, both from the perspective of fingerprint detection, and the potential to gain further intelligence from this type of evidence.

Gaiani, G, Diogène, J & Campàs, M 2023, 'Addressing Ciguatera Risk Using Biosensors for the Detection of Gambierdiscus and Ciguatoxins' in The Handbook of Environmental Chemistry, Springer International Publishing, Switzerland, pp. 21-46.
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Ciguatera fish poisoning (CFP) is one of the most relevant seafood-borne diseases worldwide. It is caused by the ingestion of seafood contaminated with ciguatoxins (CTXs), potent marine neurotoxins produced by microalgae of the genera Gambierdiscus and Fukuyoa. These genera are endemic of the tropical and subtropical areas of the world, but in recent times are being found more and more in temperate areas, such as the Mediterranean Sea. In order to properly assess and manage CFP risk, the detection of Gambierdiscus/Fukuyoa species and the discrimination between toxic and non-toxic fish specimens are crucial. To tackle these challenges, biosensors have recently been developed for the detection not only of CTXs in fish and microalgae samples but also of the DNA of the responsible microalgae in the environment. These tools are sensitive, specific, rapid, robust, reliable, easy to use, and they could represent a step forward towards in situ detection, helping in the CFP risk management and protecting human health.

Guo, X, Wang, S, Gao, H, Zang, R, Zhang, X, Yang, J, Wang, C & Wang, G 2023, 'Cathode Materials for Sodium-Ion Batteries' in Handbook of Sodium-Ion Batteries, Jenny Stanford Publishing, pp. 63-181.
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Jacka, L, Lindsay, J, Dowd, A & Naidu, S 2023, 'Hybrid and Flexible Learning' in Porter, DB, Campbell, C, Logan-Fleming, D & Jones, H (eds), Bringing the Australasian Technology and Practice Trends into Focus: The 2022–2023 Contextualising Horizon Report, ASCILITE.

Kelty, S, Green, N, Ribaux, O, Roux, C & Robertson, J 2023, 'Assessment of Occupational Stress' in Encyclopedia of Forensic Sciences, Third Edition, Elsevier, pp. 209-220.
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Krosch, MN, Johnston, NP, Archer, M & Wallman, JF 2023, 'Forensic Entomology' in Forensic and Legal Medicine, CRC Press, pp. 977-984.
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McNevin, D & Padula, M 2023, 'Serology: Blood' in Encyclopedia of Forensic Sciences, Third Edition, Elsevier, pp. 470-483.
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Mishra, N, Bhatt, S, Paudel, KR, Hansbro, PM & Dua, K 2023, 'Preface', pp. v-vi.

Murray, ML & Murray, BR 2023, 'Phytoremediation of Agricultural Pollutants in the Tropics' in Wetlands for Remediation in the Tropics. Wetlands: Ecology, Conservation and Management, Springer, Cham, Switzerland, pp. 117-133.

Nguyen, D-V, Nguyen, T-T, Adha, RS, Zheng, L, Bui, X-T, Ma, X & Vo, HNP 2023, 'Forward osmosis: Principle and applications in sustainable water and energy development' in Current Developments in Biotechnology and Bioengineering, Elsevier, The Netherlands, pp. 463-491.
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The global demand for freshwater is predicted to increase up to 30% by 2050. Therefore, water reuse/desalination for production of clean water and energy development are critically important. In the meantime, the forward osmosis (FO) membrane is an emerging process with the expectation of overcoming the challenges of the conventional pressure-driven membrane processes to achieve energy-efficient and sustainable water treatment. Herein this chapter introduces the theory of the forward osmosis process (definition, concept, and modeling equations for water flux, reverse solute flux prediction). Some critical factors (Temp, pH, FS, DS, CFV, configurations, etc.) affecting the performance of the FO membrane are presented systematically. In addition, the book chapter covers a summary of FO applications to the main sectors: desalination, wastewater treatment, water reuse, concentration of materials (juice, milk, algae, sludge, medicine, etc.), resource recovery (N, P, oil, heavy metals, etc.), agricultural fertigation, and energy generation. The chapter is expected to provide the readerships with a basic understanding of the FO process and its application to sustainable water and energy development.

Nienaber, C, Forbes, SL, Connor, M, Wescott, DJ, Ward, J, Steadman, DW & Colman, KL 2023, 'Forensic Taphonomy' in Encyclopedia of Forensic Sciences, Third Edition, Elsevier, pp. 700-711.
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Nucera, F, Salvato, I, Ricciardi, L, Col, JD, Monaco, F, Hansbro, PM, Adcock, IM, Casolaro, V, Stellato, C & Caramori, G 2023, 'RNA-binding Proteins as a New Link Between COPD and Lung Cancer' in Interdisciplinary Cancer Research, Springer International Publishing.
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Popovic, A, Roux, C & Morelato, M 2023, 'Illicit Drugs and Pharmaceuticals Analysis' in Chemometric Methods in Forensic Science, Royal Society of Chemistry, pp. 39-64.
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Over the years, chemometrics has been increasingly proposed and used in the field of forensic science. This trend can be seen in the area of illicit drugs and pharmaceuticals. A variety of analyses (both qualitative and quantitative) are performed on illicit drugs and pharmaceuticals, leading to complex and often multi-dimensional datasets. The use of chemometrics, combined with the correct interpretation of the results, can provide additional information to aid decisions regarding crime disruption, prevention and reduction. Of particular interest in this chapter is the generation and analysis of drug profiles that often contain high-dimensional data that needs to be processed and interpreted in a systematic manner. Chemometrics can highlight patterns and trends in the data that relate to essential questions regarding classification and discrimination of specimens, for example classifying illicit drug seizures into chemical classes based on profile similarity or discriminating counterfeit pharmaceuticals from their authentic counterparts. This chapter provides a literature review of the most common chemometric methods used in drug profiling, with a particular focus on pattern recognition methods.

Reimers, JR & McKemmish, LK 2023, 'Conceptual Understanding of Mixed‐Valence Compounds and Its Extension to General Stereoisomerism' in Mixed-Valence Systems: Fundamentals, Synthesis, Electron Transfer, and Applications, Wiley, Germany, pp. 45-91.
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Isomerism in mixed-valence compounds is usually interpreted semi-quantitatively using the coupled harmonic oscillator model introduced by Hush. This review first considers the primary qualitative scenarios envisaged by his model: the weak-coupling regime in which non-adiabatic effects become critical, the intermediate-coupling regime typical of most chemical systems, the regime in which anharmonicity is critical, the strong-coupling regime typical of delocalized mixed-valence compounds, and the inverted regime in which reactions slow down with increasing exothermicity. In particular, different observable features, including, structural, spectroscopic, kinetic, Stark-effect, electrochemical, and spin resonance effects, are associated with each scenario. Extensions of the theory are then reviewed that facilitate applications to more general unimolecular isomerization processes. Treated uniformly, specific applications are then reviewed pertaining to traditional mixed-valence complexes including Prussian blue and the Creutz–Taube ion, primary charge separation during bacterial photosynthesis and in artificial devices, charge transport in molecular conductors, hydrogen bonding, the ammonia inversion reaction, identification of the primary feature causing the chemistry of first-row elements to differ so much from that of the later rows, and aromaticity.

Ross, PM, Scanes, E, Byrne, M, Ainsworth, TD, Donelson, JM, Foo, SA, Hutchings, P, Thiyagarajan, V & Parker, LM 2023, 'Surviving the Anthropocene: The Resilience of Marine Animals to Climate Change' in Oceanography and Marine Biology, CRC Press, pp. 35-80.
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If marine organisms are to persist through the Anthropocene, they will need to be resilient, but what is resilience, and can resilience of marine organisms build within a single lifetime or over generations? The aim of this review is to evaluate the resilience capacity of marine animals in a time of unprecedented global climate change. Resilience is the capacity of an ecosystem, society, or organism to recover from stress. Marine organisms can build resilience to climate change through phenotypic plasticity or adaptation. Phenotypic plasticity involves phenotypic changes in physiology, morphology, or behaviour which improve the response of an organism in a new environment without altering their genotype. Adaptation is an evolutionary longer process, occurring over many generations and involves the selection of tolerant genotypes which shift the average phenotype within a population towards the fitness peak. Research on resilience of marine organisms has concentrated on responses to specific species and single climate change stressors. It is unknown whether phenotypic plasticity and adaptation of marine organisms including molluscs, echinoderms, polychaetes, crustaceans, corals, and fish will be rapid enough for the pace of climate change.

Roux, C & Jones, K 2023, 'Paper Analysis' in Encyclopedia of Forensic Sciences, Third Edition, Elsevier, pp. 88-99.
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Scanes, E, Shalders, TC, Coleman, MA, Champion, C, Benkendorff, K, Joyce, PWS, Middleton, J, Cunsolo, A, Harper, S, Falkenberg, LJ & Dupont, S 2023, 'Chapter 10 Climate change and the ocean' in Oceans and Human Health, Elsevier, pp. 265-288.
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Sharma, K, Paudel, KR, Panth, N, Jha, SK & Devkota, HP 2023, 'Targeting vascular inflammation in atherosclerosis with plant extracts, phytochemicals, and their advanced drug formulations' in Recent Developments in Anti-Inflammatory Therapy, Elsevier, pp. 107-112.
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Spindler, X & Frick, AA 2023, 'Visualization of Fingerprints' in Encyclopedia of Forensic Sciences, Third Edition, Elsevier, The Netherlands, pp. 811-820.
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Visualization of latent fingerprints is carried out using a variety of optical, physical, chemical and physico-chemical methods. The technique(s) applied typically depend on the porosity of the surface (substrate), beginning with optical techniques and proceeding to more elaborate or destructive methods as necessary. While a vast range of visualization methods are currently available for routine use, constant developments are required to meet ongoing challenges including the proliferation of new surface types, availability of key reagents and the needs of jurisdictions with limited resources.

Verma, NK, Naik, RR, Wong, BHS, Jayaraman, A, Fazil, MHUT, Lim, KY, Cheam, MS, Yuan, JCX, Ting, JKY, Mamidi, A, Lakshminarayanan, R, Lai, KO, Wong, JH, Fairley, LH, Salvatore Vincent, A, Qi, CLZ, Verma, R & Barron, AM 2023, 'Rare autoimmune and autoinflammatory neurologic disorders' in Translational Neuroimmunology, Volume 7, Elsevier, pp. 189-219.
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Ward, J & Watherston, J 2023, 'Quantitative and qualitative assessment of DNA recovered from human skeletal remains' in Forensic Genetic Approaches for Identification of Human Skeletal Remains, Elsevier, UK, pp. 137-163.
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This chapter introduces DNA quantification and the importance of assessing the quantity and quality of DNA recovered from human skeletal remains to ensure optimal performance of downstream assays. Quantification methods and instruments commonly used by forensic laboratories are presented, with a focus on real-time quantitative PCR (qPCR) techniques. The suitability of each qPCR method for determining the amount of amplifiable total human, male, and/or mitochondrial DNA, and for detecting the presence of co-extracted inhibitors or degraded DNA, is discussed. Finally, explanations on how this quantitative and qualitative sample information should be utilized to guide selection of genetic markers, DNA input amount, and procedural modifications for addressing sample degradation and inhibition are provided.

Ward, J, Watherston, J, Kahline, I, McMahon, TP & Edson, SM 2023, 'Genotyping and sequencing of DNA recovered from human skeletal remains using capillary electrophoresis (CE)' in Forensic Genetic Approaches for Identification of Human Skeletal Remains, Elsevier, UK, pp. 285-323.
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This chapter introduces capillary electrophoresis (CE) and how it is used for profiling DNA recovered from human skeletal remains. It will explain the most common fragment analysis and sequencing applications employed in forensic genetics, including the genotyping of autosomal short tandem repeats (STRs) and Sanger sequencing of mitochondrial DNA (mtDNA). The process of how PCR products are prepared, injected, separated, detected, and interpreted is discussed for each application. The CE platforms, chemistries, and analysis software commonly used by forensic laboratories are presented. Sample-specific CE artifacts often associated with skeletal samples are also detailed. Finally, the advantages and disadvantages of CE will be highlighted given the growing popularity of massively parallel sequencing (MPS).

Watherston, J & Ward, J 2023, 'Autosomal short tandem repeat (STR) profiling of human skeletal remains' in Forensic Genetic Approaches for Identification of Human Skeletal Remains, Elsevier, The Netherlands, pp. 167-197.
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This chapter introduces autosomal short tandem repeats (STRs) and their use as the most popular genetic marker for human identification. It explains the characteristics of STR loci that make them suitable for forensic use and lists the core STR loci currently used for DNA profiling. Commercial STR multiplexes and thermal cycling instruments commonly used by forensic laboratories are presented, and the applicability of each for profiling of human skeletal remains is discussed. PCR conditions that can be modified to improve STR profiling results from challenging human skeletal samples are also detailed. Finally, technologies that facilitate high-throughput and/or rapid STR profiling for large-scale identification efforts are explored.

Wen, S, Bao, G & Jin, D 2023, 'Advanced optical properties of upconversion nanoparticles' in Encyclopedia of Nanomaterials, Elsevier, pp. 613-648.
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Wen, S, Bao, G & Jin, D 2023, 'Advanced optical properties of upconversion nanoparticles' in Encyclopedia of Nanomaterials, p. V1-613-V1-648.
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Upconversion nanoparticles (UCNPs) are typically doped with lanthanide ions, capable of converting near-infrared light into visible and ultraviolet emissions. Their unique optical properties have attracted considerable research interests and enabled various applications ranging from molecular detection, bioimaging, nanomedicine, to volumetric displays and microcavity lasers. By overcoming the restraint of concentration quenching and controlled synthesis of heterogeneous structures, UCNPs become sufficiently bright with versatile multifunctions. This article surveys the recent advances in developing UCNPs and highlights their optical properties for emerging applications.

Zhang, J, Zhao, Y, Guo, X, Chen, C, Dong, C-L, Liu, R-S, Han, C-P, Li, Y, Gogotsi, Y & Wang, G 2023, 'Single Platinum Atoms Immobilized on an MXene as an Efficient Catalyst for the Hydrogen Evolution Reaction' in MXenes, Jenny Stanford Publishing, pp. 829-852.
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A. Anwar, S, Srivastava, A & Zerouali, B 2023, 'On the role of land-surface hydrology schemes in simulating the daily maximum and minimum air temperatures of Australia using a regional climate model (RegCM4)', Journal of Water and Climate Change, vol. 14, no. 3, pp. 989-1011.
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AbstractThe present study addresses the possible effects of soil moisture changes on the simulated daily maximum and minimum air temperatures of Australia for a duration of 13 years. Therefore, the community land model version 4.5 (CLM4.5; coupled to the RegCM4) was used to represent the soil moisture and processes associated with it. The CLM4.5 has two land-surface hydrology schemes: TOPMODEL (TOP) and Variable Infiltration Capacity (VIC) and two simulations were conducted, namely: TOP and VIC. The results showed that VIC has lower soil moisture than TOP, leading to a decrease in vegetation transpiration, evaporation, and an increase in soil evaporation relative to TOP. However, there is no considerable difference between the two simulations compared with reanalysis products. In comparison to in-situ measurements, the RegCM4 can reasonably model the climatological annual cycle of mean air temperature (TMP) and its performance varies with the study site (e.g., RegCM4 overestimates TMP by 2.76 and 5.46 °C at Yanco and Tumbarumba, respectively). In summary, the simulated maximum and minimum air temperatures are sensitive to the physical parameterization of RegCM4 rather than variations in soil moisture. Likewise, improvements to the land-surface hydrology schemes TOP/VIC are required to better model Australia's daily maximum and minimum air temperatures.

Abdullah, A, Szkuta, B & Meakin, GE 2023, 'Effect of swabbing technique and duration on forensic DNA recovery', Science & Justice, vol. 63, no. 3, pp. 343-348.
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Adabifiroozjaei, E, Rastkerdar, E, Nemoto, Y, Nakayama, Y, Nishimiya, Y, Fronzi, M, Yao, Y, Nguyen, MT, Molina-Luna, L & Suzuki, TS 2023, 'In-situ scanning transmission electron microscopy study of Al-amorphous SiO2 layer-SiC interface', Journal of Materials Science, vol. 58, no. 6, pp. 2456-2468.
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AbstractHere, we present a comprehensive study on atomic-scale in-situ biasing/heating scanning transmission electron microscopy ((S)TEM) of Al-amorphous SiO2–SiC interface. The investigation includes electrical, chemical, and structural analysis of the interface at different temperatures (25–600 °C). The results show that at ~ 500 °C the electrical (three-orders of magnitude resistivity drop), chemical (dissolution of SiO2amorphous layer), and microstructural features (e.g.formation of Al2O3, Si and Al4C3) of the interface start to change. According to the results, amorphous SiO2dissolves in Al, leading to formation of α-Al2O3and Si within the Al. In contrast, elemental interdiffusion (Al3+ ⇄ Si4+) between Al and SiC occurs resulting in formation of Al4C3. From the results, we can infer that reaction mechanism between Al and crystalline SiC is different with that between Al and SiO2amorphous phase. It is believed that structural similarities between SiC and Al4C3play an important role in paving the way for elemental interdiffusion.

Adhikari, S, Mahmud, MAP, Nguyen, MD & Timms, W 2023, 'Evaluating fundamental biochar properties in relation to water holding capacity', Chemosphere, vol. 328, pp. 138620-138620.
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Ahmadimanesh, M, Etemad, L, Morshedi Rad, D, Ghahremani, MH, Mohammadpour, AH, Jafarzadeh Esfehani, R, Jowsey, P, Behdani, F, Moallem, SA & Abbaszadegan, MR 2023, 'Effect of citalopram and sertraline on the expression of miRNA- 124, 132, and 16 and their protein targets in patients with depression.', Iran J Basic Med Sci, vol. 26, no. 7, pp. 820-829.
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OBJECTIVES: This study aimed to evaluate the effect of SSRIs on the expression of miRNAs and their protein targets. MATERIALS AND METHODS: In a 100 day open-label study of citalopram (n=25) and sertraline (n=25), levels of miRNA 16, 132, and 124 and glucocorticoid receptor (GR), Brain-derived neurotrophic factor (BDNF), and serotonin transporter (SERT) protein expression were measured by QRT-PCR and western blot in healthy control (n=20), patients with depression at the baseline, and same patients after 100 days of treatment. RESULTS: Expression levels of GR and BDNF proteins were lower in the depressed group before treatment as compared with the healthy group (P<0.0001). The SERT level was higher among the depressed group before treatment in comparison with the healthy group (P<0.0001). The level of GR and BDNF significantly increased, and SERT expression decreased after receiving sertraline (P<0.05). When the depressed group received citalopram, only SERT and GR were altered (P<0.05). Among the microRNAs' expression investigated, mir-124 and mir-132 were higher, and mir-16 was lower among the depressed compared with the healthy group (P<0.0001). Individuals receiving citalopram only showed an increase in the expression of mir-16 while administration of sertraline led to a significant increase in the expression of mir-16 and a decrease in mir-124 and mir-132 (P<0.05). CONCLUSION: This elucidated the relationship between antidepressant treatment and the expression of different microRNA that control gene expression in various pathways involved in depressed patients. Receiving SSRI can affect the level of these proteins and their relevant microRNAs.

Aisbett, J, Drinkwater, EJ, Quarrie, KL & Woodcock, S 2023, 'Applying generalized funnel plots to help design statistical analyses', Statistical Papers, vol. 64, no. 1, pp. 355-364.
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AbstractResearchers across many fields routinely analyze trial data using Null Hypothesis Significance Tests with zero null and p < 0.05. To promote thoughtful statistical testing, we propose a visualization tool that highlights practically meaningful effects when calculating sample sizes. The tool re-purposes and adapts funnel plots, originally developed for meta-analyses, after generalizing them to cater for meaningful effects. As with traditional sample size calculators, researchers must nominate anticipated effect sizes and variability alongside the desired power. The advantage of our tool is that it simultaneously presents sample sizes needed to adequately power tests for equivalence, for non-inferiority and for superiority, each considered at up to three alpha levels and in positive and negative directions. The tool thus encourages researchers at the design stage to think about the type and level of test in terms of their research goals, costs of errors, meaningful effect sizes and feasible sample sizes. An R-implementation of the tool is available on-line.

Ajani, PA, Savela, H, Kahlke, T, Harrison, D, Jeffries, T, Kohli, GS, Verma, A, Laczka, O, Doblin, MA, Seymour, JR, Larsson, ME, Potts, J, Scanes, P, Gribben, PE, Harrison, L & Murray, SA 2023, 'Response of planktonic microbial assemblages to disturbance in an urban sub-tropical estuary', Water Research, vol. 243, pp. 120371-120371.
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Microbes are sensitive indicators of estuarine processes because they respond rapidly to dynamic disturbance events. As most of the world's population lives in urban areas and climate change-related disturbance events are becoming more frequent, estuaries bounded by cities are experiencing increasing stressors, at the same time that their ecosystem services are required more than ever. Here, using a multidisciplinary approach, we determined the response of planktonic microbial assemblages in response to seasonality and a rainfall disturbance in an urban estuary bounded by Australia's largest city, Sydney. We used molecular barcoding (16S, 18S V4 rRNA) and microscopy-based identification to compare microbial assemblages at locations with differing characteristics and urbanisation histories. Across 142 samples, we identified 8,496 unique free-living bacterial zOTUs, 8,175 unique particle associated bacterial zOTUs, and 1,920 unique microbial eukaryotic zOTUs. Using microscopy, we identified only the top <10% abundant, larger eukaryotic taxa (>10 µm), however quantification was possible. The site with the greater history of anthropogenic impact showed a more even community of associated bacteria and eukaryotes, and a significant increase in dissolved inorganic nitrogen following rainfall, when compared to the more buffered site. This coincided with a reduced proportional abundance of Actinomarina and Synechococcus spp., a change in SAR 11 clades, and an increase in the eukaryotic microbial groups Dinophyceae, Mediophyceae and Bathyoccocaceae, including a temporary dominance of the harmful algal bloom dinoflagellate Prorocentrum cordatum (syn. P. minimum). Finally, a validated hydrodynamic model of the estuary supported these results, showing that the more highly urbanised and upstream location consistently experienced a higher magnitude of salinity reduction in response to rainfall events during the study period. The best abiotic variables to explain commu...

Akter, A, Kakizaki, T, Itabashi, E, Kunita, K, Shimizu, M, Akter, MA, Mehraj, H, Okazaki, K, Dennis, ES & Fujimoto, R 2023, 'Characterization of FLOWERING LOCUS C 5 in Brassica rapa L.', Molecular Breeding, vol. 43, no. 8.
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AbstractBrassica rapa L., which includes Chinese cabbage, turnip, and pak choi, has more complex flowering time regulation than does Arabidopsis thaliana due to the presence of multiple paralogous flowering time genes. FLOWERING LOCUS C (FLC) is one of the key genes regulating the flowering time, and B. rapa has four FLC paralogs. BrFLC5 on the reference genome is deemed a pseudogene because of a mutation (from G to A) in the splice site of the third intron, but there are some accessions with a G nucleotide in the splice site. In this study, we genotyped 310 B. rapa accessions and found that 19 had homozygous and 81 had heterozygous putative functional BrFLC5 alleles. Accessions of turnip showed the highest proportion with a functional BrFLC5 allele. BrFLC5 acts as a floral repressor when overexpressed in A. thaliana. The BrFLC5 expression level varied in pre-vernalized plants, and this transcriptional variation was not associated with the G/A polymorphism in the third intron. Three accessions having a higher BrFLC5 expression in pre-vernalized plants had a 584-bp insertion in the promoter region. Many regions homologous to this 584-bp sequence are present in the B. rapa genome, and this 584-bp inserted region has tandem duplications of an AT-rich sequence in its central region. The possibility that a high expression of a functional BrFLC5 could contribute to producing premature bolting-resistant lines in B. rapa vegetables is discussed.

Akter, MA, Miyaji, N, Shimizu, M, Takasaki-Yasuda, T, Dennis, ES & Fujimoto, R 2023, 'The role of salicylic acid responsive genes in disease resistance in Brassica rapa vegetable', Acta Horticulturae, no. 1362, pp. 305-312.
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Alhamami, T, Roy Chowdhury, P, Venter, H, Veltman, T, Truswell, A, Abraham, S, Sapula, SA, Carr, M, Djordjevic, SP & Trott, DJ 2023, 'Genomic profiling of Pasteurella multocida isolated from feedlot cases of bovine respiratory disease', Veterinary Microbiology, vol. 283, pp. 109773-109773.
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Pasteurella multocida causes a range of diseases in many host species throughout the world, including bovine respiratory disease (BRD) which is predominantly seen in feedlot cattle. This study assessed genetic diversity among 139 P. multocida isolates obtained from post-mortem lung swabs of BRD-affected feedlot cattle in four Australian states: New South Wales, Queensland, South Australia, and Victoria during 2014-2019. Whole-genome sequencing (WGS) was used to determine capsular serogroup, lipopolysaccharide genotypes, multi-locus sequence types and phylogenetic relationships. Two capsular types (A and D), with most isolates (132/139; 95%) belonging to type A; and three lipopolysaccharide (LPS) genotypes were identified (L1 [6/139; 4.3%], L3 [124/139; 89.2%] and L6 [9/139; 6.4%)]). Multi-locus sequence types (STs) ST9, ST13, ST17, ST20, ST36, ST50, ST58, ST79, ST124, ST125, ST132, ST167, ST185, ST327, ST394, and three novel STs [ST396, ST397, and ST398] were identified, with ST394 (59/139; 42.4%) and ST79 (44/139; 32%) the most prevalent in all four states. Isolates displaying phenotypic resistance to single, dual or multiple antibiotics (macrolide, tetracycline and aminopenicillins) were predominantly ST394 (23/139; 17%). Laterally mobile elements identified in the resistant ST394 isolates included small plasmids, encoding macrolide and/or tetracycline resistance, distributed in all states; and chromosomally located integrative conjugative elements (ICEs) (4 ST394 and 1 ST125) from the same Queensland feedlot. This study highlights the genomic diversity, epidemiological relationships and AMR associations in bovine P. multocida isolates from Australia and provides insight into the unique ST prevalence compared to other major beef-producing countries.

Alharbi, KS, Javed Shaikh, MA, Imam, SS, Alshehri, S, Ghoneim, MM, Almalki, WH, Singh, SK, Kumar, D, Kumar, AP, Dua, K, Chellappan, DK, Paudel, KR & Gupta, G 2023, 'Role of Flavonoids in Management of Various Biological Targets inAlzheimer’s Disease: Evidence from Preclinical to Clinical Studies', Current Medicinal Chemistry, vol. 30, no. 18, pp. 2061-2074.
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Abstract:More than 10 million people worldwide have Alzheimer's disease (AD), a degenerative neurological illness and the most prevalent form of dementia. AD's progression in memory loss, cognitive deterioration, and behavioral changes are all symptoms. Amyloid-beta 42 (Aβ42), the hyperphosphorylated forms of microtubule-associated tau protein, and other cellular and systemic alterations are all factors that contribute to cognitive decline in AD. Rather than delivering a possible cure, present therapy strategies focus on reducing disease symptoms. It has long been suggested that various naturally occurring small molecules (plant extract products and microbiological isolates, for example) could be beneficial in preventing or treating disease. Small compounds, such as flavonoids, have attracted much interest recently due to their potential to alleviate cellular stress. Flavonoids have been proven helpful in various ways, including antioxidants, anti-inflammatory agents, and anti-apoptotic agents, but their mechanism remains unknown. The flavonoid therapy of Alzheimer's disease focuses on this review, which includes a comprehensive literature analysis.

Alijani, H, Reineck, P, Komljenovic, R, Russo, SP, Low, MX, Balendhran, S, Crozier, KB, Walia, S, Nash, GR, Yeo, LY & Rezk, AR 2023, 'The Acoustophotoelectric Effect: Efficient Phonon–Photon–Electron Coupling in Zero-Voltage-Biased 2D SnS₂ for Broad-Band Photodetection', ACS Nano, vol. 17, no. 19, pp. 19254-19264.
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Al‐Juboori, A, Zeng, HZJ, Nguyen, MAP, Ai, X, Laucht, A, Solntsev, A, Toth, M, Malaney, R & Aharonovich, I 2023, 'Quantum Key Distribution Using a Quantum Emitter in Hexagonal Boron Nitride', Advanced Quantum Technologies, vol. 6, no. 9.
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AbstractQuantum key distribution (QKD) is considered the most immediate application to be widely implemented among a variety of potential quantum technologies. QKD enables sharing secret keys between distant users by using photons as information carriers. An ongoing endeavor is to implement these protocols in practice in a robust, and compact manner so as to be efficiently deployable in a range of real‐world scenarios. Single photon sources (SPS) in solid‐state materials are prime candidates in this respect. This article demonstrates a room temperature, discrete‐variable quantum key distribution system using a bright single photon source in hexagonal‐boron nitride, operating in free‐space. Employing an easily interchangeable photon source system, keys with one million bits length, and a secret key of approximately 70000 bits, at a quantum bit error rate of 6%, with ε‐security of 10−10 are generated. This study demonstrates the first proof of concept finite‐key BB84 QKD system realized with hBN defects.

Allam, VSRR, Pavlidis, S, Liu, G, Kermani, NZ, Simpson, J, To, J, Donnelly, S, Guo, Y-K, Hansbro, PM, Phipps, S, Morand, EF, Djukanovic, R, Sterk, P, Chung, KF, Adcock, I, Harris, J & Sukkar, MB 2023, 'Macrophage migration inhibitory factor promotes glucocorticoid resistance of neutrophilic inflammation in a murine model of severe asthma', Thorax, vol. 78, no. 7, pp. 661-673.
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BackgroundSevere neutrophilic asthma is resistant to treatment with glucocorticoids. The immunomodulatory protein macrophage migration inhibitory factor (MIF) promotes neutrophil recruitment to the lung and antagonises responses to glucocorticoids. We hypothesised that MIF promotes glucocorticoid resistance of neutrophilic inflammation in severe asthma.MethodsWe examined whether sputum MIF protein correlated with clinical and molecular characteristics of severe neutrophilic asthma in the Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes (U-BIOPRED) cohort. We also investigated whether MIF regulates neutrophilic inflammation and glucocorticoid responsiveness in a murine model of severe asthma in vivo.ResultsMIF protein levels positively correlated with the number of exacerbations in the previous year, sputum neutrophils and oral corticosteroid use across all U-BIOPRED subjects. Further analysis of MIF protein expression according to U-BIOPRED-defined transcriptomic-associated clusters (TACs) revealed increased MIF protein and a corresponding decrease in annexin-A1 protein in TAC2, which is most closely associated with airway neutrophilia and NLRP3 inflammasome activation. In a murine model of severe asthma, treatment with the MIF antagonist ISO-1 significantly inhibited neutrophilic inflammation and increased glucocorticoid responsiveness. Coimmunoprecipitation studies using lung tissue lysates demonstrated that MIF directly interacts with and cleaves annexin-A1, potentially reducing its biological activity.ConclusionOur data suggest that MIF promotes glucocorticoid-resistance of neutrophilic inflammation by reducing the biological activity of annexin-A1, a potent glucocorticoid-regulated protein that inhi...

Alobeedallah, H, Cornell, B, Ghazal, M & Coster, H 2023, 'The Effect of Benzyl Alcohol on the Voltage-Current Characteristics of Tethered Lipid Bilayers', The Journal of Membrane Biology, vol. 256, no. 4-6, pp. 423-431.
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Alqudah, A, AbuDalo, R, Qnais, E, Wedyan, M, Oqal, M & McClements, L 2023, 'The emerging importance of immunophilins in fibrosis development', Molecular and Cellular Biochemistry, vol. 478, no. 6, pp. 1281-1291.
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AbstractImmunophilins are a family of proteins encompassing FK506-binding proteins (FKBPs) and cyclophilins (Cyps). FKBPs and Cyps exert peptidyl-prolyl cis-trans isomerase (PPIase) activity, which facilitates diverse protein folding assembly, or disassembly. In addition, they bind to immunosuppressant medications where FKBPs bind to tacrolimus (FK506) and rapamycin, whereas cyclophilins bind to cyclosporin. Some large immunophilins have domains other than PPIase referred to as tetratricopeptide (TPR) domain, which is involved in heat shock protein 90 (Hsp90) and heat shock protein 70 (Hsp 70) chaperone interaction. The TPR domain confers immunophilins’ pleotropic actions to mediate various physiological and biochemical processes. So far, immunophilins have been implicated to play an important role in pathophysiology of inflammation, cancer and neurodegenerative disorders. However, their importance in the development of fibrosis has not yet been elucidated. In this review we focus on the pivotal functional and mechanistic roles of different immunophilins in fibrosis establishment affecting various organs. The vast majority of the studies reported that cyclophilin A, FKBP12 and FKBP10 likely induce organ fibrosis through the calcineurin or TGF-β pathways. FKBP51 demonstrated a role in myelofibrosis development through calcineurin-dependant pathway, STAT5 or NF-κB pathways. Inhibition of these specific immunophilins has been shown to decrease the extent of fibrosis suggesting that immunophilins could be a novel promising therapeutic target to prevent or reverse fibrosis.

Ambrose, SJ, Hamidian, M & Hall, RM 2023, 'The extensively antibiotic resistant ST111 Acinetobacter baumannii isolate RBH2 carries an extensive mobile element complement of plasmids, transposons and insertion sequences', Plasmid, vol. 128, pp. 102707-102707.
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The complete genome of RBH2, a sporadic, carbapenem resistant ST111 Acinetobacter baumannii isolate from Brisbane, Australia was determined and analysed. RBH2 is extensively resistant and the chromosome includes two transposons carrying antibiotic resistance genes, AbaR4 (oxa23 in Tn2006) and Tn7::Tn2006 (dfrA1, sat2, aadA1, oxa23). The chromosome also includes two copies of Tn6175, a transposon carrying putative copper resistance genes, and 1-17 copies of six different insertion sequences. RBH2 has six plasmids ranging in size from 6 kb - 141 kb, four carrying antibiotic resistance genes. Plasmids pRBH2-1 (aadB) and pRBH2-2 (aphA6 in TnaphA6) were found to be essentially identical to known plasmids pRAY*-v1 and pS21-1, respectively. The largest plasmids, pRBH2-5 (oxa23 in AbaR4) and pRBH2-6 (oxa23 in AbaR4::ISAba11 and sul2, tet(B), strA and strB in Tn6172) have known transfer-proficient relatives. pRBH2-5, an RP-T1 (RepAci6) plasmid, also carries a different putative copper resistance transposon related to Tn6177 found in pS21-2. The backbone of pRBH2-5 is related to those of previously described RepAci6 plasmids pAb-G7-2 and pA85-3 but has some distinctive features. Three different RepAci6 backbone types were distinguished, Type 1 (pAb-G7-2), Type 2 (pA85-3) and Type 3 (pRBH2-5 and pS21-2). pRBH2-6 is closely related to pAB3 and their backbones differ by only 5 SNPs. Plasmids pRBH2-3 and pRBH2-4 do not carry antibiotic resistance genes. pRBH2-3 does not include an identifiable rep gene and is a novel plasmid type. pRBH2-4 is of the R3-T3 type and includes segments of the larger pABTJ2 that heads this group. Other ST111 genomes carry different plasmids.

Andersson, J, Kleinheinz, D, Ramach, U, Kiesenhofer, N, Ashenden, A, Valtiner, M, Holt, S, Koeper, I, Schmidpeter, PAM & Knoll, W 2023, 'Native Function of the Bacterial Ion Channel SthK in a Sparsely Tethered Lipid Bilayer Membrane Architecture', The Journal of Physical Chemistry B, vol. 127, no. 16, pp. 3641-3650.
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Anwar, SA, Malcheva, K & Srivastava, A 2023, 'Estimating the potential evapotranspiration of Bulgaria using a high-resolution regional climate model', Theoretical and Applied Climatology, vol. 152, no. 3-4, pp. 1175-1188.
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Ariyama, N, Pardo-Roa, C, Muñoz, G, Aguayo, C, Ávila, C, Mathieu, C, Almonacid, LI, Medina, RA, Brito, B, Johow, M & Neira, V 2023, 'Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus in Wild Birds, Chile', Emerging Infectious Diseases, vol. 29, no. 9, pp. 1842-1845.
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Armbrecht, L, Focardi, A, Lawler, K, O’Brien, P, Leventer, A, Noble, TL, Opdyke, B, Duffy, M, Evangelinos, D, George, SC, Lieser, J, López‐Quirós, A, Post, A, Ostrowski, M, Paulsen, I & Armand, L 2023, 'From the Surface Ocean to the Seafloor: Linking Modern and Paleo‐Genetics at the Sabrina Coast, East Antarctica (IN2017_V01)', Journal of Geophysical Research: Biogeosciences, vol. 128, no. 4.
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AbstractWith ongoing climate change, research into the biological changes occurring in particularly vulnerable ecosystems, such as Antarctica, is critical. The Totten Glacier region, Sabrina Coast, is currently experiencing some of the highest rates of thinning across all East Antarctica. An assessment of the microscopic organisms supporting the ecosystem of the marginal sea‐ice zone over the continental rise is important, yet there is a lack of knowledge about the diversity and distribution of these organisms throughout the water column, and their occurrence and/or preservation in the underlying sediments. Here, we provide a taxonomic overview of the modern and ancient marine bacterial and eukaryotic communities of the Totten Glacier region, using a combination of 16S and 18S rRNA amplicon sequencing (modern DNA) and shotgun metagenomics (sedimentary ancient DNA, sedaDNA). Our data show considerable differences between eukaryote and bacterial signals in the water column versus the sediments. Proteobacteria and diatoms dominate the bacterial and eukaryote composition in the upper water column, while diatoms, dinoflagellates, and haptophytes notably decrease in relative abundance with increasing water depth. Little diatom sedaDNA is preserved in the sediments, which are instead dominated by Proteobacteria and Retaria. We compare the diatom microfossil and sedaDNA record and link the weak preservation of diatom sedaDNA to DNA degradation while sinking through the water column to the seafloor. This study provides the first assessment of DNA transfer from ocean waters to sediments and an overview of the microscopic communities occurring in the climatically important Totten Glacier region.

Ashique, S, Gupta, K, Gupta, G, Mishra, N, Singh, SK, Wadhwa, S, Gulati, M, Dureja, H, Zacconi, F, Oliver, BG, Paudel, KR, Hansbro, PM, Chellappan, DK & Dua, K 2023, 'Vitamin D—A prominent immunomodulator to prevent COVID‐19 infection', International Journal of Rheumatic Diseases, vol. 26, no. 1, pp. 13-30.
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AbstractCOVID‐19 remains a life‐threatening infectious disease worldwide. Several bio‐active agents have been tested and evaluated in an effort to contain this disease. Unfortunately, none of the therapies have been successful, owing to their safety concerns and the presence of various adverse effects. Various countries have developed vaccines as a preventive measure; however, they have not been widely accepted as effective strategies. The virus has proven to be exceedingly contagious and lethal, so finding an effective treatment strategy has been a top priority in medical research. The significance of vitamin D in influencing many components of the innate and adaptive immune systems is examined in this study. This review aims to summarize the research on the use of vitamin D for COVID‐19 treatment and prevention. Vitamin D supplementation has now become an efficient option to boost the immune response for all ages in preventing the spread of infection. Vitamin D is an immunomodulator that treats infected lung tissue by improving innate and adaptive immune responses and downregulating the inflammatory cascades. The preventive action exerted by vitamin D supplementation (at a specific dose) has been accepted by several observational research investigations and clinical trials on the avoidance of viral and acute respiratory dysfunctions. To assess the existing consensus about vitamin D supplementation as a strategy to treat and prevent the development and progression of COVID‐19 disease, this review intends to synthesize the evidence around vitamin D in relation to COVID‐19 infection.

Asmara, AP, Chen, H & Ung, AT 2023, 'Preventing Adipogenesis and Preserving Mitochondria and GLUT-4 Functions by Extracts and Isolated Compounds of Australian Acacia saligna', Molecules, vol. 28, no. 18, pp. 6677-6677.
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Acacia saligna’s secondary metabolites show promise in treating type 2 diabetes mellitus and its related conditions. We previously discovered that methanolic extracts, isolated flavonoids, and cyclitols effectively preserve mitochondria in 3T3-L1 adipocytes. In this current work, quantification of lipid droplet levels with Oil Red O assay showed a noticeable decrease in lipogenesis in 3T3-L1 cells. Methanolic leaf and bark extracts and isolated compounds, (−)-epicatechin 6 and myricitrin 8, reduced cellular lipid levels by 21.15% to 25.28%, respectively. mRNA levels of key regulators of mitochondrial biogenesis, such as adiponectin, PGC-1α, and mtTFA, were increased. Methanolic flower extract (FL-MeOH) and its chemical components, naringenin 1 and D-(+)-pinitol 5a, increased these gene levels from 10% to 29% at the higher dose. Our study found that FL-MeOH slightly reduced pro-inflammatory cytokines TNF-α and IL-6, attributed to two phytochemicals, naringenin-7-O-α-L-arabinofuranoside 2 and D-(+)-pinitol 5a. Western blot analysis also showed that adipocytes treated with MeOH extracts had higher GLUT-4 expression levels than untreated adipocytes. Overall, A. saligna extracts and their isolated compounds demonstrated anti-lipogenesis activity during 3T3-L1 cell differentiation, modulation of transcriptional levels of adiponectin, PGC-1α, and mtTFA, reducing TNF-α and IL-6 mRNA levels, promoting mitochondrial biogenesis, and enhancing GLUT-4 expression.

Asmara, AP, Prasansuklab, A, Chiabchalard, A, Chen, H & Ung, AT 2023, 'Antihyperglycemic Properties of Extracts and Isolated Compounds from Australian Acacia saligna on 3T3-L1 Adipocytes', Molecules, vol. 28, no. 10, pp. 4054-4054.
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Our early work indicated that methanolic extracts from the flowers, leaves, bark, and isolated compounds of Acacia saligna exhibited significant antioxidant activities in vitro. The overproduction of reactive oxygen species (ROS) in the mitochondria (mt-ROS) interfered with glucose uptake, metabolism, and its AMPK-dependent pathway, contributing to hyperglycemia and diabetes. This study aimed to screen the ability of these extracts and isolated compounds to attenuate the production of ROS and maintain mitochondrial function via the restoration of mitochondrial membrane potential (MMP) in 3T3-L1 adipocytes. Downstream effects were investigated via an immunoblot analysis of the AMPK signalling pathway and glucose uptake assays. All methanolic extracts effectively reduced cellular ROS and mt-ROS levels, restored the MMP, activated AMPK-α, and enhanced cellular glucose uptake. At 10 µM, (−)-epicatechin-6 (from methanolic leaf and bark extracts) markedly reduced ROS and mt-ROS levels by almost 30% and 50%, respectively, with an MMP potential ratio 2.2-fold higher compared to the vehicle control. (−)-Epicatechin 6 increased the phosphorylation of AMPK-α by 43%, with an 88% higher glucose uptake than the control. Other isolated compounds include naringenin 1, naringenin-7-O-α-L-arabinopyranoside 2, isosalipurposide 3, D-(+)-pinitol 5a, and (−)-pinitol 5b, which also performed relatively well across all assays. Australian A. saligna active extracts and compounds can reduce ROS oxidative stress, improve mitochondrial function, and enhance glucose uptake through AMPK-α activation in adipocytes, supporting its potential antidiabetic application.

Asmara, AP, Prasansuklab, A, Tencomnao, T & Ung, AT 2023, 'Identification of Phytochemicals in Bioactive Extracts of Acacia saligna Growing in Australia.', Molecules, vol. 28, no. 3, pp. 1028-1028.
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Acacia saligna growing in Australia has not been fully investigated for its bioactive phytochemicals. Sequential polarity-based extraction was employed to provide four different extracts from individual parts of A. saligna. Bioactive extracts were determined using in vitro antioxidant and yeast α-glucosidase inhibitory assays. Methanolic extracts from barks, leaves, and flowers are the most active and have no toxicity against 3T3-L1 adipocytes. Compound isolation of bioactive extracts provided us with ten compounds. Among them are two novel natural products; naringenin-7-O-α-L-arabinopyranoside 2 and (3S*,5S*)-3-hydroxy-5-(2-aminoethyl) dihydrofuran-2(3H)-one 9. D-(+)-pinitol 5a (from barks and flowers), (-)-pinitol 5b (exclusively from leaf), and 2,4-di-t-butylphenol 7 are known natural products and new to A. saligna. (-)-Epicatechin 6, quercitrin 4, and myricitrin 8 showed potent antioxidant activities consistently in DPPH and ABTS assays. (-)-Epicatechin 6 (IC50 = 63.58 μM),D-(+)-pinitol 5a (IC50 = 74.69 μM), and naringenin 1 (IC50 = 89.71 μM) are the strong inhibitors against the α-glucosidase enzyme. The presence of these compounds supports the activities exerted in our methanolic extracts. The presence of 2,4-di-t-butylphenol 7 may support the reported allelopathic and antifungal activities. The outcome of this study indicates the potential of Australian A. saligna as a rich source of bioactive compounds for drug discovery targeting type 2 diabetes.

Attia, J, Horvat, JC, Hunter, T, Hansbro, PM, Hure, A, Peel, R, Ren, S, Dizon, J, Chiu, S, Srikusalanukul, W, Greenough, R, Abhayaratna, WP, Ren, S, Hansbro, PM, Peel, R, Srikusalanukul, W, Abhayaratna, W, Newby, D, Hure, A, D’Este, C, Tonkin, A, Hopper, I, Levi, C, Sturm, J, Durrheim, D, Hung, J, Briffa, T, Chew, D, Anderson, P, Moon, L, McEvoy, M & Attia, J 2023, 'Persistence of Detectable Anti-Pneumococcal Antibodies 4 Years After Pneumococcal Polysaccharide Vaccination in a Randomised Controlled Trial: The Australian Study for the Prevention through Immunisation of Cardiovascular Events (AUSPICE)', Heart, Lung and Circulation, vol. 32, no. 11, pp. 1378-1385.
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Awatade, N, Wark, P, Chan, A, Mamun, SM, Mohd Esa, N, Matsunaga, K, Rhee, C, Hansbro, P & Sohal, S 2023, 'The Complex Association between COPD and COVID-19', Journal of Clinical Medicine, vol. 12, no. 11, pp. 3791-3791.
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Chronic obstructive pulmonary disease (COPD) is significant cause of morbidity and mortality worldwide. There is mounting evidence suggesting that COPD patients are at increased risk of severe COVID-19 outcomes; however, it remains unclear whether they are more susceptible to acquiring SARS-CoV-2 infection. In this comprehensive review, we aim to provide an up-to-date perspective of the intricate relationship between COPD and COVID-19. We conducted a thorough review of the literature to examine the evidence regarding the susceptibility of COPD patients to COVID-19 infection and the severity of their disease outcomes. While most studies have found that pre-existing COPD is associated with worse COVID-19 outcomes, some have yielded conflicting results. We also discuss confounding factors such as cigarette smoking, inhaled corticosteroids, and socioeconomic and genetic factors that may influence this association. Furthermore, we review acute COVID-19 management, treatment, rehabilitation, and recovery in COPD patients and how public health measures impact their care. In conclusion, while the association between COPD and COVID-19 is complex and requires further investigation, this review highlights the need for careful management of COPD patients during the pandemic to minimize the risk of severe COVID-19 outcomes.

Awatade, NT, Reid, AT, Nichol, KS, Budden, KF, Veerati, PC, Pathinayake, PS, Grainge, CL, Hansbro, PM & Wark, PAB 2023, 'Comparison of commercially available differentiation media on cell morphology, function, and anti-viral responses in conditionally reprogrammed human bronchial epithelial cells', Scientific Reports, vol. 13, no. 1, p. 11200.
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AbstractPrimary air liquid interface (ALI) cultures of bronchial epithelial cells are used extensively to model airway responses. A recent advance is the development of conditional reprogramming that enhances proliferative capability. Several different media and protocols are utilized, yet even subtle differences may influence cellular responses. We compared the morphology and functional responses, including innate immune responses to rhinovirus infection in conditionally reprogrammed primary bronchial epithelial cells (pBECs) differentiated using two commonly used culture media. pBECs collected from healthy donors (n = 5) were CR using g-irradiated 3T3 fibroblasts and Rho Kinase inhibitor. CRpBECs were differentiated at ALI in either PneumaCult (PN-ALI) or bronchial epithelial growth medium (BEGM)-based differentiation media (BEBM:DMEM, 50:50, Lonza)—(AB-ALI) for 28 days. Transepithelial electrical resistance (TEER), immunofluorescence, histology, cilia activity, ion channel function, and expression of cell markers were analyzed. Viral RNA was assessed by RT-qPCR and anti-viral proteins quantified by LEGENDplex following Rhinovirus-A1b infection. CRpBECs differentiated in PneumaCult were smaller and had a lower TEER and cilia beat frequency compared to BEGM media. PneumaCult media cultures exhibited increased FOXJ1 expression, more ciliated cells with a larger active area, increased intracellular mucins, and increased calcium-activated chloride channel current. However, there were no significant changes in viral RNA or host antiviral responses. There are distinct structural and functional differences in pBECs cultured in the two commonly used ALI differentiation media. Such factors need to be taken into consideration when designing CRpBECs ALI experiments for specific research questions.

Bai, L, Song, A, Wang, L, Lei, X, Zhang, T, Tian, H, Liu, H, Qin, X, Wang, G & Shao, G 2023, 'Enhancement of hydrogen desorption for electrocatalytic hydrogen evolution on nickel-coupled graphite carbon nitride catalysts', Ionics, vol. 29, no. 1, pp. 323-330.
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Bailey, RL, Jun, S, Cowan, AE, Eicher-Miller, HA, Gahche, JJ, Dwyer, JT, Hartman, TJ, Mitchell, DC, Seguin-Fowler, RA, Carroll, RJ & Tooze, JA 2023, 'Major Gaps in Understanding Dietary Supplement Use in Health and Disease', Annual Review of Nutrition, vol. 43, no. 1, pp. 179-197.
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Precise dietary assessment is critical for accurate exposure classification in nutritional research, typically aimed at understanding how diet relates to health. Dietary supplement (DS) use is widespread and represents a considerable source of nutrients. However, few studies have compared the best methods to measure DSs. Our literature review on the relative validity and reproducibility of DS instruments in the United States [e.g., product inventories, questionnaires, and 24-h dietary recalls (24HR)] identified five studies that examined validity ( n = 5) and/or reproducibility ( n = 4). No gold standard reference method exists for validating DS use; thus, each study's investigators chose the reference instrument used to measure validity. Self-administered questionnaires agreed well with 24HR and inventory methods when comparing the prevalence of commonly used DSs. The inventory method captured nutrient amounts more accurately than the other methods. Reproducibility (over 3 months to 2.4 years) of prevalence of use estimates on the questionnaires was acceptable for common DSs. Given the limited body of research on measurement error in DS assessment, only tentative conclusions on these DS instruments can be drawn at present. Further research is critical to advancing knowledge in DS assessment for research and monitoring purposes.

Balzer, MJ, Hitchcock, JN, Hadwen, WL, Kobayashi, T, Westhorpe, DP, Boys, C & Mitrovic, SM 2023, 'Experimental additions of allochthonous dissolved organic matter reveal multiple trophic pathways to stimulate planktonic food webs', Freshwater Biology, vol. 68, no. 5, pp. 821-836.
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AbstractThere is still considerable debate as to whether the allochthonous (terrestrial) dissolved organic matter (DOM) mobilised during large flow events plays an important role in supporting secondary production in riverine food webs. Understanding how food webs respond to large pulses of terrestrial DOM (tDOM) is important for conceptualising the relative importance of energy sources supporting food webs.A mesocosm experiment (1,000 L) using three concentrations of leachate (1, 4, 8 mg C/L and a control) made from floodplain DOM was run for 34 days in a dam filled with water from Gunbower Creek in Northern Victoria, Australia. Nutrients, phytoplankton, zooplankton and stable isotope (δ13C signatures) data were collected to examine how floodplain nutrients affected growth and community structure within the lower food web typical of an Australian lowland river.All leachate additions led to very high concentrations of zooplankton and mixotrophic algae compared to the control. Mixotrophs dominated the algal biovolume of all leachate additions until Day (D)20 and appeared to drive changes in δ13C signatures of particulate organic matter (POM) which were significantly related to changes in zooplankton δ13C signatures. tDOM additions did not significantly suppress obligate autotroph growth which also appeared important as a food source, as reflected in the δ13C signatures of zooplankton and POM after D10.These results show the ability of phytoplankton and zooplankton communities in lowland rivers to respond quickly to changes in resource availability and quality. Mixotrophs appeared to provide an important trophic link between allochthonous carbon and ...

Bani Saeid, A, Patel, VK, Mehndiratta, S, Rajput, R, Kundu, RK, Singh, SK, Chellappan, DK, Kokkinis, S, De Rubis, G, Collet, T, Paudel, KR, Hansbro, PM & Dua, K 2023, 'Dissecting the in vitro fate of plant-derived bioactive encapsulated nanoparticles in lung diseases', Food Bioscience, vol. 56, pp. 103205-103205.
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Bartels, N, Dilernia, NJ, Howlett, L & Camp, EF 2023, 'Stress event for “super corals” in Great Barrier Reef mangrove lagoon', Marine Biodiversity, vol. 53, no. 5.
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Bates, H, Zavafer, A, Szabó, M & Ralph, PJ 2023, 'The slow-phase of chlorophyll fluorescence induction curve reflects the electron transport rates of Photosystem II in vivo in Chlorella vulgaris', Journal of Applied Phycology, vol. 35, no. 1, pp. 109-116.
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Becchi, S, Chieng, B, Bradfield, LA, Capellán, R, Leung, BK & Balleine, BW 2023, 'Cognitive effects of thalamostriatal degeneration are ameliorated by normalizing striatal cholinergic activity', Science Advances, vol. 9, no. 25.
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The loss of neurons in parafascicular thalamus (Pf) and their inputs to dorsomedial striatum (DMS) in Lewy body disease (LBD) and Parkinson’s disease dementia (PDD) have been linked to the effects of neuroinflammation. We found that, in rats, these inputs were necessary for both the function of striatal cholinergic interneurons (CINs) and the flexible encoding of the action-outcome (AO) associations necessary for goal-directed action, producing a burst-pause pattern of CIN firing but only during the remapping elicited by a shift in AO contingency. Neuroinflammation in the Pf abolished these changes in CIN activity and goal-directed control after the shift in contingency. However, both effects were rescued by either the peripheral or the intra-DMS administration of selegiline, a monoamine oxidase B inhibitor that we found also enhances adenosine triphosphatase activity in CINs. These findings suggest a potential treatment for the cognitive deficits associated with neuroinflammation affecting the function of the Pf and related structures.

Becker, A, Lowry, MB, Fowler, AM & Taylor, MD 2023, 'Hydroacoustic surveys reveal the distribution of mid-water fish around two artificial reef designs in temperate Australia', Fisheries Research, vol. 257, pp. 106509-106509.
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Beckley, A, Wang, J & Birch, P 2023, 'Are organisational responses by police forces appropriate to adequately safeguard police officer wellness? A review of the scientific evidence', Safer Communities, vol. 22, no. 4, pp. 312-326.
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PurposeA central tenet for safer communities is having a healthy police force. This study aims to understand what police forces should and need to be doing to safeguard police officer wellness by examining the existing scientific evidence on police well-being.Design/methodology/approachDrawing on the Scale for the Assessment of Narrative Articles, this paper has adopted a case study approach to examine effective practices and approaches for safeguarding police officer wellness.FindingsThe research presented in this paper yields fours themes, providing contemporary evidence for responding to and safeguarding police officer wellness.Practical implicationsThis paper yields several implications for policy and practice. An evidence-based approach to be adopted by policing organisations for dealing with police officer wellness. An improvement to police officer support and prevention of stigma towards those who are suffering from poor mental health. Training for police managers in dealing with police officer wellness. Continuous monitoring and evaluation of police organisation efficacy in dealing with police officer wellness.Originality/valueMuch has been written about police officer mental health and well-being over the past decade, yet arguably, there has been limited attention paid to assessing the evidence and making sense of what this growing volume of research is advocating. This paper seeks to address this deficit in the research and provide a review of the published researc...

Bey, E, Hughes, C, Hogg, K, Chance, R & Petrou, K 2023, 'Ocean acidification reduces iodide production by the marine diatom Chaetoceros sp. (CCMP 1690)', Marine Chemistry, vol. 257, pp. 104311-104311.
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Bhadauria, AS, Dhungana, HN, Verma, V, Woodcock, S & Rai, T 2023, 'Studying the efficacy of isolation as a control strategy and elimination of tuberculosis in India: A mathematical model', Infectious Disease Modelling, vol. 8, no. 2, pp. 458-470.
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Bhaskaran, A & Wand, MP 2023, 'Dispersion parameter extension of precise generalized linear mixed model asymptotics', Statistics & Probability Letters, vol. 193, pp. 109691-109691.
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Billings, JL, Hilton, JBW, Liddell, JR, Hare, DJ & Crouch, PJ 2023, 'Fundamental Neurochemistry Review: Copper availability as a potential therapeutic target in progressive supranuclear palsy: Insight from other neurodegenerative diseases', Journal of Neurochemistry, vol. 167, no. 3, pp. 337-346.
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AbstractSince the first description of Parkinson's disease (PD) over two centuries ago, the recognition of rare types of atypical parkinsonism has introduced a spectrum of related PD‐like diseases. Among these is progressive supranuclear palsy (PSP), a neurodegenerative condition that clinically differentiates through the presence of additional symptoms uncommon in PD. As with PD, the initial symptoms of PSP generally present in the sixth decade of life when the underpinning neurodegeneration is already significantly advanced. The causal trigger of neuronal cell loss in PSP is unknown and treatment options are consequently limited. However, converging lines of evidence from the distinct neurodegenerative conditions of PD and amyotrophic lateral sclerosis (ALS) are beginning to provide insights into potential commonalities in PSP pathology and opportunity for novel therapeutic intervention. These include accumulation of the high abundance cuproenzyme superoxide dismutase 1 (SOD1) in an aberrant copper‐deficient state, associated evidence for altered availability of the essential micronutrient copper, and evidence for neuroprotection using compounds that can deliver available copper to the central nervous system. Herein, we discuss the existing evidence for SOD1 pathology and copper imbalance in PSP and speculate that treatments able to provide neuroprotection through manipulation of copper availability could be applicable to the treatment of PSP.image

Bordin, DM, Bishop, D, de Campos, EG, Blanes, L, Doble, P, Roux, C & De Martinis, BS 2023, 'Analysis of Stimulants in Sweat and Urine Using Disposable Pipette Extraction and Gas Chromatography Coupled to Mass Spectrometry in the Context of Doping Control', Journal of Analytical Toxicology, vol. 46, no. 9, pp. 991-998.
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AbstractUrine is initially collected from athletes to screen for the presence of illicit drugs. Sweat is an alternative sample matrix that provides advantages over urine including reduced opportunity for sample adulteration, longer detection-time window and non-invasive collection. Sweat is suitable for analysis of the parent drug and metabolites. In this study, a method was developed and validated to determine the presence of 13 amphetamine- and cocaine-related substances and their metabolites in sweat and urine using disposable pipette extraction (DPX) by gas chromatography coupled to mass spectrometry. The DPX extraction was performed using 0.1 M HCl and dichloromethane:isopropanol:ammonium hydroxide (78:20:2, v/v/v) followed by derivatization with N-methyl-N-(trimethylsilyl) trifluoroacetamide at 90°C for 20 min. DPX extraction efficiencies ranged between 65.0% and 96.0% in urine and 68.0% and 101.0% in sweat. Method accuracy was from 90.0% to 104.0% in urine and from 89.0% to 105.0% in sweat. Intra-assay precision in urine and in sweat were &lt;15.6% and &lt;17.8%, respectively, and inter-assay precision ranged from 4.70% to 15.3% in urine and from 4.05% to 15.4% in sweat. Calibration curves presented a correlation coefficient –0.99 for all analytes in both matrices. The validated method was applied to urine and sweat samples collected from 40 professional athletes who knowingly took one or more of the target illicit drugs. Thirteen of 40 athletes were positive for at least one drug. All the drugs detected in the urine were also detected in sweat samples indicating that sweat is a viable matrix for screening or confirmatory drug testing.

Brennan, LE, Kumawat, LK, Piatek, ME, Kinross, AJ, McNaughton, DA, Marchetti, L, Geraghty, C, Wynne, C, Tong, H, Kavanagh, ON, O’Sullivan, F, Hawes, CS, Gale, PA, Kavanagh, K & Elmes, RBP 2023, 'Potent antimicrobial effect induced by disruption of chloride homeostasis', Chem, vol. 9, no. 11, pp. 3138-3158.
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Brito, BP, Frost, MJ, Anantanawat, K, Jaya, F, Batterham, T, Djordjevic, SP, Chang, W-S, Holmes, EC, Darling, AE & Kirkland, PD 2023, 'Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics', Microbiome, vol. 11, no. 1, p. 158.
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Abstract Background Bovine respiratory disease (BRD) is one of the most common diseases in intensively managed cattle, often resulting in high morbidity and mortality. Although several pathogens have been isolated and extensively studied, the complete infectome of the respiratory complex consists of a more extensive range unrecognised species. Here, we used total RNA sequencing (i.e., metatranscriptomics) of nasal and nasopharyngeal swabs collected from animals with and without BRD from two cattle feedlots in Australia. Results A high abundance of bovine nidovirus, influenza D, bovine rhinitis A and bovine coronavirus was found in the samples. Additionally, we obtained the complete or near-complete genome of bovine rhinitis B, enterovirus E1, bovine viral diarrhea virus (sub-genotypes 1a and 1c) and bovine respiratory syncytial virus, and partial sequences of other viruses. A new species of paramyxovirus was also identified. Overall, the most abundant RNA virus, was the bovine nidovirus. Characterisation of bacterial species from the transcriptome revealed a high abundance and diversity of Mollicutes in BRD cases and unaffected control animals. Of the non-Mollicutes species, Histophilus somni was detected, whereas there was a low abundance of Mannheimia haemolytica. Conclusion This study highlights the use of untargeted sequencing approaches to study the unrecognised range of microorganisms present in healthy or diseased animals and the need to study previously uncultured viral species that may have an important role in cattle respiratory disease. ...

Brito, L, Sahade, V, Weber, B, Bersch‐Ferreira, ÂC, Marcadenti, A, Torreglosa, C, Kovacs, C, Moreira, ASB, Torres, RDS, Marinho, H, Matos, C, Abib, R, Souza, GC, Shirmann, GDS, Nagano, FEZ, Ramos, MEM, Poloni, S, El Kik, RM, Feres, NH, Dutra, ES, Ferreira Carvalho, APP, David, MM, Galvão, I, Sousa, ACS, Dantas, CDF, Gonçalves, A, Pinheiro, JMF, Vasconcelos, SML, Penafort, A, de Oliveira Carlos, DM, Luna, A, Neto, JADF, Dias, L, Moriguchi, EH, Bruscato, N, Izar, MC, Lopes, S, Backes, LM, Bressan, J, Raimondi, S, Kumbier, M & Daltro, C 2023, 'Factors associated with diet quality among Brazilian individuals with cardiovascular diseases', Journal of Human Nutrition and Dietetics, vol. 36, no. 5, pp. 1713-1726.
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AbstractBackgroundAn individual's dietary pattern contributes in different ways to the prevention and control of recurrent cardiovascular events. However, the quality of the diet is influenced by several factors. The present study aimed to evaluate the quality of the diet of individuals with cardiovascular diseases and determine whether there is an association between sociodemographic and lifestyle factors.MethodsThis is a cross‐sectional study carried out with individuals with atherosclerosis (coronary artery disease, cerebrovascular disease or peripheral arterial disease) recruited from 35 reference centres for the treatment of cardiovascular disease in Brazil. Diet quality was assessed according to the Modified Alternative Healthy Eating Index (mAHEI) and stratified into tertiles. For comparing two groups, the Mann–Whitney or Pearson's chi‐squared tests were used. However, for comparing three or more groups, analysis of variance or Kruskal–Wallis was used. For the confounding analysis, a multinomial regression model was used. p < 0.05 was considered statistically significant.ResultsIn total, 2360 individuals were evaluated: 58.5% male and 64.2% elderly. The median (interquartile range [IQR]) of the mAHEI was 24.0 (20.0–30.0), ranging from 0.4 to 56.0 points. When comparing the odds ratios (ORs) for the low (first tertile) and medium (second tertile) diet quality groups with the high‐quality group (third tertile), it was observed that there was an association between diet quality with a family income of 1.885 (95% confidence intervals [CI] = 1.302–2.729) and 1.566 (95% CI = 1.097–2.235), as well as physical activity of 1.391 (95% CI = 1.107–1.749) and 1.346 (95% CI = 1.086–1.667), respectively. In addition, associations were observ...

Brockbals, L, Garrett-Rickman, S, Fu, S, Ueland, M, McNevin, D & Padula, MP 2023, 'Estimating the time of human decomposition based on skeletal muscle biopsy samples utilizing an untargeted LC–MS/MS-based proteomics approach', Analytical and Bioanalytical Chemistry, vol. 415, no. 22, pp. 5487-5498.
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AbstractAccurate estimation of the postmortem interval (PMI) is crucial in forensic medico-legal investigations to understand case circumstances (e.g. narrowing down list of missing persons or include/exclude suspects). Due to the complex decomposition chemistry, estimation of PMI remains challenging and currently often relies on the subjective visual assessment of gross morphological/taphonomic changes of a body during decomposition or entomological data. The aim of the current study was to investigate the human decomposition process up to 3 months after death and propose novel time-dependent biomarkers (peptide ratios) for the estimation of decomposition time. An untargeted liquid chromatography tandem mass spectrometry–based bottom-up proteomics workflow (ion mobility separated) was utilized to analyse skeletal muscle, collected repeatedly from nine body donors decomposing in an open eucalypt woodland environment in Australia. Additionally, general analytical considerations for large-scale proteomics studies for PMI determination are raised and discussed. Multiple peptide ratios (human origin) were successfully proposed (subgroups < 200 accumulated degree days (ADD), < 655 ADD and < 1535 ADD) as a first step towards generalised, objective biochemical estimation of decomposition time. Furthermore, peptide ratios for donor-specific intrinsic factors (sex and body mass) were found. Search of peptide data against a bacterial database did not yield any results most likely due to the low abundance of bacterial proteins within the collected human biopsy samples. For comprehensive time-dependent modelling, increased donor number would be necessary along with targeted confirmation of proposed peptides. Overall, the presented results provide valuable information that aid in the understanding and estimation of the human decomposition processes. Graphical Abstract

Broome, ST, Mandwie, M, Gorrie, CA, Musumeci, G, Marzagalli, R & Castorina, A 2023, 'Early Alterations of PACAP and VIP Expression in the Female Rat Brain Following Spinal Cord Injury', Journal of Molecular Neuroscience, vol. 73, no. 9-10, pp. 724-737.
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AbstractPrevious evidence shows that rapid changes occur in the brain following spinal cord injury (SCI). Here, we interrogated the expression of the neuropeptides pituitary adenylyl cyclase-activating peptide (PACAP), vasoactive intestinal peptides (VIP), and their binding receptors in the rat brain 24 h following SCI. Female Sprague-Dawley rats underwent thoracic laminectomy; half of the rats received a mild contusion injury at the level of the T10 vertebrate (SCI group); the other half underwent sham surgery (sham group). Twenty-four hours post-surgery, the hypothalamus, thalamus, amygdala, hippocampus (dorsal and ventral), prefrontal cortex, and periaqueductal gray were collected. PACAP, VIP, PAC1, VPAC1, and VPAC2 mRNA and protein levels were measured by real-time quantitative polymerase chain reaction and Western blot. In SCI rats, PACAP expression was increased in the hypothalamus (104–141% vs sham) and amygdala (138–350%), but downregulated in the thalamus (35–95%) and periaqueductal gray (58–68%). VIP expression was increased only in the thalamus (175–385%), with a reduction in the amygdala (51–68%), hippocampus (40–75%), and periaqueductal gray (74–76%). The expression of the PAC1 receptor was the least disturbed by SCI, with decrease expression in the ventral hippocampus (63–68%) only. The expression levels of VPAC1 and VPAC2 receptors were globally reduced, with more prominent reductions of VPAC1 vs VPAC2 in the amygdala (21–70%) and ventral hippocampus (72–75%). In addition, VPAC1 downregulation also extended to the dorsal hippocampus (69–70%). These findings demonstrate that as early as 24 h post-SCI, there are region-specific disruptions of PACAP, VIP, and related receptor transcript and protein levels in supraspinal regions controlling higher cognitive functions.

Brown, A, Lamb, E, Deo, A, Pasin, D, Liu, T, Zhang, W, Su, S & Ueland, M 2023, 'The use of novel electronic nose technology to locate missing persons for criminal investigations', iScience, vol. 26, no. 4, pp. 106353-106353.
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The search for missing persons is a major challenge for investigations involving presumed deceased individuals. Currently, the most effective tool is the use of cadaver-detection dogs; however, they are limited by their cost, limited operation times, and lack of granular information reported to the handler. Thus, there is a need for discrete, real-time detection methods that provide searchers explicit information as to whether human-decomposition volatiles are present. A novel e-nose (NOS.E) developed in-house was investigated as a tool to detect a surface-deposited individual over time. The NOS.E was able to detect the victim throughout most stages of decomposition and was influenced by wind parameters. The sensor responses from different chemical classes were compared to chemical class abundance confirmed by two-dimensional gas chromatography - time-of-flight mass spectrometry. The NOS.E demonstrated its ability to detect surface-deposited individuals days and weeks since death, demonstrating its utility as a detection tool.

Brown, AO, Frankham, GJ, Stuart, BH & Ueland, M 2023, 'Assessing the impact of habitat and captivity status on volatilome profiles of the illegally traded shingleback, Tiliqua rugosa', Forensic Science International: Animals and Environments, vol. 4, pp. 100071-100071.
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Brown, AO, Green, PJ, Frankham, GJ, Stuart, BH & Ueland, M 2023, 'Insights into the Effects of Violating Statistical Assumptions for Dimensionality Reduction for Chemical “-omics” Data with Multiple Explanatory Variables', ACS Omega, vol. 8, no. 24, pp. 22042-22054.
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Brown, AO, Ueland, M, Stuart, BH & Frankham, GJ 2023, 'A forensically validated genetic toolkit for the species and lineage identification of the highly trafficked shingleback lizard (Tiliqua rugosa)', Forensic Science International: Genetics, vol. 62, pp. 102784-102784.
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Shingleback lizards (Tiliqua rugosa) are among the most trafficked native fauna from Australia in the illegal pet trade. There are four morphologically recognised subspecies of shinglebacks, all with differing overseas market values. Shinglebacks from different geographic locales are often trafficked and housed together, which may complicate identifying the State jurisdiction where the poaching event occurred. Additionally, shinglebacks can be housed and trafficked with other species within the same genus, which may complicate DNA analysis, especially in scenarios where indirect evidence (e.g. swabs, faeces) is taken for analysis. In this study, a forensic genetic toolkit was designed and validated to target shingleback DNA for species identification and geographic origin. To do this, field sampling across Australia was conducted to expand the phylogeographic sampling of shinglebacks across their species range and include populations suspected to be poaching hotspots. A commonly used universal reptile primer set (ND4/LEU) was then validated for use in forensic casework related to the genus Tiliqua. Two additional ND4 primer sets were designed and validated. The first primer set was designed and demonstrated to preferentially amplify an ∼510 bp region of the genus Tiliqua over other reptiles and builds on existing data to expand the available phylogeographic database. The second primer set was designed and demonstrated to solely amplify an ∼220 bp region of T. rugosa ND4 over any other reptile species. Through the validation process, all primers were demonstrated to amplify T. rugosa DNA from a variety of sample types (e.g. degraded, low quality and mixed). Two of the primer sets were able to distinguish the genetic lineage of T. rugosa from the phylogeographic database. This work provides the first forensically validated toolkit and phylogeographic genetic database for Squatmate lizards.

Brunet, M, Le Duff, N, Rigaut‐Jalabert, F, Romac, S, Barbeyron, T & Thomas, F 2023, 'Seasonal dynamics of a glycan‐degrading flavobacterial genus in a tidally mixed coastal temperate habitat', Environmental Microbiology, vol. 25, no. 12, pp. 3192-3206.
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AbstractCoastal marine habitats constitute hotspots of primary productivity. In temperate regions, this is due both to massive phytoplankton blooms and dense colonisation by macroalgae that mostly store carbon as glycans, contributing substantially to local and global carbon sequestration. Because they control carbon and energy fluxes, algae‐degrading microorganisms are crucial for coastal ecosystem functions. Environmental surveys revealed consistent seasonal dynamics of alga‐associated bacterial assemblages, yet resolving what factors regulate the in situ abundance, growth rate and ecological functions of individual taxa remains a challenge. Here, we specifically investigated the seasonal dynamics of abundance and activity for a well‐known alga‐degrading marine flavobacterial genus in a tidally mixed coastal habitat of the Western English Channel. We show that members of the genus Zobellia are a stable, low‐abundance component of healthy macroalgal microbiota and can also colonise particles in the water column. This genus undergoes recurring seasonal variations with higher abundances in winter, significantly associated to biotic and abiotic variables. Zobellia can become a dominant part of bacterial communities on decaying macroalgae, showing a strong activity and high estimated in situ growth rates. These results provide insights into the seasonal dynamics and environmental constraints driving natural populations of alga‐degrading bacteria that influence coastal carbon cycling.

Bubathi, V, Leslie, L, Speer, M, Hartigan, J, Wang, J & Gupta, A 2023, 'Impact of Accelerated Climate Change on Maximum Temperature Differences between Western and Coastal Sydney', Climate, vol. 11, no. 4, pp. 76-76.
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The aims of this study are to assess the impacts of accelerated climate change on summer maximum temperatures since the early 1990s in the Australian city of Sydney’s eastern coastal and western inland suburbs. Western Sydney currently experiences far more intense summer (December–March) heat waves than coastal Sydney, with maximum temperatures exceeding those of coastal Sydney by up to 10 °C. Aside from increased bushfire danger, extreme temperature days pose health and socio-economic threats to western Sydney. Permutation tests of consecutive summer periods, 1962–1991 and 1992–2021, are employed to determine the differential climate change impacts on maximum summer temperatures at two locations: Sydney and Richmond, representative of eastern and western Sydney, respectively. Attribution of observed maximum summer temperature trends in Sydney and Richmond was performed using machine learning techniques applied to known Australian region oceanic and atmospheric climate drivers. It was found that there is a marked disparity in the percentage of summer days above the 95th percentile during the accelerated climate change period (1992–2021) between Richmond (+35%) and Sydney (−24%), relative to 1962–1991. The climate drivers detected as attributes were similar in both Sydney and Richmond, but, unsurprisingly, Sydney was more affected than Richmond by the oceanic climate drivers.

Buckley, T, Karanam, K, Han, H, Vo, HNP, Shukla, P, Firouzi, M & Rudolph, V 2023, 'Effect of different co-foaming agents on PFAS removal from the environment by foam fractionation', Water Research, vol. 230, pp. 119532-119532.
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Buckley, T, Vuong, T, Karanam, K, Vo, PHN, Shukla, P, Firouzi, M & Rudolph, V 2023, 'Using foam fractionation to estimate PFAS air-water interface adsorption behaviour at ng/L and µg/L concentrations', Water Research, vol. 239, pp. 120028-120028.
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Budden, KF, Gellatly, SL, Vaughan, A, Amorim, N, Horvat, JC, Hansbro, NG, Wood, DLA, Hugenholtz, P, Dennis, PG, Wark, PAB & Hansbro, PM 2023, 'Probiotic Bifidobacterium longum subsp. longum Protects against Cigarette Smoke-Induced Inflammation in Mice', International Journal of Molecular Sciences, vol. 24, no. 1, pp. 252-252.
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Bifidobacterium are prominent gut commensals that produce the short-chain fatty acid (SCFA) acetate, and they are often used as probiotics. Connections between the gut and the lung, termed the gut–lung axis, are regulated by the microbiome. The gut–lung axis is increasingly implicated in cigarette smoke-induced diseases, and cigarette smoke exposure has been associated with depletion of Bifidobacterium species. In this study, we assessed the impact of acetate-producing Bifidobacterium longum subsp. longum (WT) and a mutant strain with an impaired acetate production capacity (MUT) on cigarette smoke-induced inflammation. The mice were treated with WT or MUT B. longum subsp. longum and exposed to cigarette smoke for 8 weeks before assessments of lung inflammation, lung tissue gene expression and cecal SCFAs were performed. Both strains of B. longum subsp. longum reduced lung inflammation, inflammatory cytokine expression and adhesion factor expression and alleviated cigarette smoke-induced depletion in caecum butyrate. Thus, the probiotic administration of B. longum subsp. longum, irrespective of its acetate-producing capacity, alleviated cigarette smoke-induced inflammation and the depletion of cecal butyrate levels.

Butterworth, NJ, Wallman, JF, Johnston, NP, Dawson, BM, Sharp-Heward, J & McGaughran, A 2023, 'The blowfly Chrysomya latifrons inhabits fragmented rainforests, but shows no population structure', Oecologia, vol. 201, no. 3, pp. 703-719.
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AbstractClimate change and deforestation are causing rainforests to become increasingly fragmented, placing them at heightened risk of biodiversity loss. Invertebrates constitute the greatest proportion of this biodiversity, yet we lack basic knowledge of their population structure and ecology. There is a compelling need to develop our understanding of the population dynamics of a wide range of rainforest invertebrates so that we can begin to understand how rainforest fragments are connected, and how they will cope with future habitat fragmentation and climate change. Blowflies are an ideal candidate for such research because they are widespread, abundant, and can be easily collected within rainforests. We genotyped 188 blowflies (Chrysomya latifrons) from 15 isolated rainforests and found high levels of gene flow, a lack of genetic structure between rainforests, and low genetic diversity – suggesting the presence of a single large genetically depauperate population. This highlights that: (1) the blowfly Ch. latifrons inhabits a ~ 1000 km stretch of Australian rainforests, where it plays an important role as a nutrient recycler; (2) strongly dispersing flies can migrate between and connect isolated rainforests, likely carrying pollen, parasites, phoronts, and pathogens along with them; and (3) widely dispersing and abundant insects can nevertheless be genetically depauperate. There is an urgent need to better understand the relationships between habitat fragmentation, genetic diversity, and adaptive potential–especially for poorly dispersing rainforest-restricted insects, as many of these may be particularly fragmented and at highest risk of local extinction.

Cain, AK & Hamidian, M 2023, 'Portrait of a killer: Uncovering resistance mechanisms and global spread of Acinetobacter baumannii', PLOS Pathogens, vol. 19, no. 8, pp. e1011520-e1011520.
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Antibiotic resistance is a growing global concern in the field of medicine as it renders bacterial infections difficult to treat and often more severe. Acinetobacter baumannii is a gram-negative bacterial pathogen causing a wide range of infections, including pneumonia, sepsis, urinary tract infections, and wound infections. A. baumannii has emerged as a significant healthcare-associated pathogen due to its high level of antibiotic resistance. The global spread of antibiotic-resistant strains of A. baumannii has resulted in limited treatment options, leading to increased morbidity and mortality rates, especially in vulnerable populations such as the elderly and immunocompromised individuals, as well as longer hospital stays and higher healthcare costs. Further complicating the situation, multi- and pan-drug-resistant strains of A. baumannii are becoming increasingly common, and these deadly strains are resistant to all or almost all available antibiotics. A. baumannii employs various clever strategies to develop antibiotic resistance, including horizontal transfer of resistance genes, overexpression of inherent efflux pumps that remove drugs from the cell, intrinsic mutations, combined with natural selection under antibiotic selective pressure leading to emergence of successful resistance clones. The typical multidrug resistance phenotype of A. baumannii is, therefore, an orchestrated collimation of all these mechanisms combined with the worldwide spread of “global clones,” rendering infections caused by this pathogen challenging to control and treat. To address the escalating problem of antibiotic resistance in A.

Calders, K, Brede, B, Newnham, G, Culvenor, D, Armston, J, Bartholomeus, H, Griebel, A, Hayward, J, Junttila, S, Lau, A, Levick, S, Morrone, R, Origo, N, Pfeifer, M, Verbesselt, J & Herold, M 2023, 'StrucNet: a global network for automated vegetation structure monitoring', Remote Sensing in Ecology and Conservation, vol. 9, no. 5, pp. 587-598.
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AbstractClimate change and increasing human activities are impacting ecosystems and their biodiversity. Quantitative measurements of essential biodiversity variables (EBV) and essential climate variables are used to monitor biodiversity and carbon dynamics and evaluate policy and management interventions. Ecosystem structure is at the core of EBVs and carbon stock estimation and can help to inform assessments of species and species diversity. Ecosystem structure is also used as an indirect indicator of habitat quality and expected species richness or species community composition. Spaceborne measurements can provide large‐scale insight into monitoring the structural dynamics of ecosystems, but they generally lack consistent, robust, timely and detailed information regarding their full three‐dimensional vegetation structure at local scales. Here we demonstrate the potential of high‐frequency ground‐based laser scanning to systematically monitor structural changes in vegetation. We present a proof‐of‐concept high‐temporal ecosystem structure time series of 5 years in a temperate forest using terrestrial laser scanning (TLS). We also present data from automated high‐temporal laser scanning that can allow upscaling of vegetation structure scanning, overcoming the limitations of a typically opportunistic TLS measurement approach. Automated monitoring will be a critical component to build a network of field monitoring sites that can provide the required calibration data for satellite missions to effectively monitor the structural dynamics of vegetation over large areas. Within this perspective, we reflect on how this network could be designed and discuss implementation pathways.

Callan, MN, Krix, D, McLean, CM, Murray, BR & Webb, JK 2023, 'Thermal Profiles of Chainsaw Hollows and Natural Hollows during Extreme Heat Events', Biology, vol. 12, no. 3, pp. 361-361.
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Loss of hollow-bearing trees threatens many hollow-dependent wildlife. To mitigate this process, artificial chainsaw-carved hollows (CHs) are often created in dead trees, yet little is known about their thermal profiles. We measured temperatures inside 13 natural hollows (8 live and 5 dead trees) and 45 CHs (5 live and 40 dead trees) in the central west of NSW, Australia, over the course of 2 summers. Maximum temperatures and daily temperature ranges within natural hollows and artificial hollows were similar in 2017–2018. Hollow temperatures were lower in thicker-walled hollows than in thinner-walled hollows. During the January 2019 heatwave, temperatures inside CHs in dead trees exceeded 4–35 °C higher than the upper limit of the thermal neutral zone of sugar gliders—for 6.2 consecutive days (range 0–9 days). CHs in dead trees provided little buffering from thermal extremes; when air temperatures peaked at 44.6 °C, CHs in dead trees were on average 2.4 °C cooler than ambient (range: 5.5 °C cooler to 1.0 °C hotter than ambient). These results show that CHs created in dead trees may not provide suitable thermal conditions for hollow-dependent marsupials during summer heatwaves. Retention of large live trees, coupled with revegetation, is crucial for conserving hollow-dependent fauna in agricultural landscapes.

Cao, X, Gao, L, Qu, J, Li, L, Xie, Y, Zhao, Y, Wang, G & Liu, H 2023, 'Modulating Electronic Structure of PtCo‐Pt_rich Nanowires with Ru atoms for Boosted Hydrogen Evolution Catalysis', Small, vol. 19, no. 41.
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AbstractRational design and development of highly efficient hydrogen evolution reaction (HER) electrocatalysts is of great significance for the development of green water electrolysis hydrogen production technology. Ru‐engineered 1D PtCo‐Ptrich nanowires (Ru‐PtrichCo NWs) are fabricated by a facile electrodeposition method. The rich Pt surface on 1D Pt3Co contributes to the fully exposed active sites and enhanced intrinsic catalytic activity (co‐engineered by Ru and Co atoms) for HER. The incorporation of Ru atoms can not only accelerate the water dissociation in alkaline condition to provide sufficient H* but also modulate the electronic structure of Pt to achieve optimized H* adsorption energy. As a result, Ru‐PtrichCo NWs have exhibited ultralow HER overpotentials (η) of 8 and 112 mV to achieve current densities of 10 and 100 mA cm−2 in 1 m KOH, respectively, which far exceed those of commercial Pt/C catalyst (η10 = 29 mV, η100 = 206 mV). Density functional theory (DFT) calculations further demonstrate that the incorporated Ru atoms possess strong water adsorption capacity (−0.52 vs −0.12 eV for Pt), facilitating water dissociation. The Pt atoms in the outermost Pt‐rich skin of Ru‐PtrichCo NWs achieve optimized H* adsorption free energy (ΔGH*) of −0.08 eV, boosting hydrogen generation.

Carbonara, K, Padula, MP & Coorssen, JR 2023, 'Quantitative assessment confirms deep proteome analysis by integrative top–down proteomics', ELECTROPHORESIS, vol. 44, no. 3-4, pp. 472-480.
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AbstractThe goal of integrative top–down proteomics (i.e., two‐dimensional gel electrophoresis [2DE] coupled with liquid chromatography and tandem mass spectrometry [LC/MS/MS]) is a routine analytical approach that fully addresses the breadth and depth of proteomes. To accomplish this, there should be no addition, removal, or modification to any constituent proteoforms. To address two‐decade old claims of protein losses during front–end proteome resolution using 2DE, here we tested an alternate rehydration method for immobilized pH gradient strips prior to isoelectric focusing (IEF; i.e., faceup compared to facedown) and quantitatively assessed losses during the front–end of 2DE (rehydration and IEF). Using a well‐established high‐resolution, quantitative 2DE protocol, there were no detectable proteoform losses using the alternate faceup rehydration method. Although there is a <0.25% total loss of proteoforms during standard facedown rehydration, it is insignificant in terms of having any effect on overall proteome resolution (i.e., total spot count and total spot signal). This report is another milestone in integrative top–down proteomics, disproving long‐held dogma in the field and confirming that quantitative front–end 2DE/LC/MS/MS is currently the only method to broadly and deeply analyze proteomes by resolving their constituent proteoforms.

Carter, DJ, Byrne, MK, Djordjevic, SP, Robertson, H, Labbate, M, Morgan, BS & Billington, L 2023, 'Personal Data for Public Benefit: The Regulatory Determinants of Social Licence for Technologically Enhanced Antimicrobial Resistance Surveillance.', J Law Med, vol. 30, no. 1, pp. 179-190.
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Technologically enhanced surveillance systems have been proposed for the task of monitoring and responding to antimicrobial resistance (AMR) in both human, animal and environmental contexts. The use of these systems is in their infancy, although the advent of COVID-19 has progressed similar technologies in response to that pandemic. We conducted qualitative research to identify the Australian public's key concerns about the ethical, legal and social implications of an artificial intelligence (AI) and machine learning-enhanced One Health AMR surveillance system. Our study provides preliminary evidence of public support for AI/machine learning-enhanced One Health monitoring systems for AMR, provided that three main conditions are met: personal health care data must be deidentified; data use and access must be tightly regulated under strong governance; and the system must generate high-quality, reliable analyses to guide trusted health care decision-makers.

Carter, DJ, Riley, B, Evans, R, Rahmani, A, Vogl, A, Stratigos, A, Brown, JJ, Robertson, H & Travaglia, J 2023, 'The Legal Needs of People Living with a Sexually Transmissible Infection or Blood-Borne Virus: Perspectives From a Sample of the Australian Sexual Health and Blood Borne Virus Workforce.', J Law Med, vol. 30, no. 3, pp. 706-715.
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Law and the legal environment are important factors in the epidemiology and prevention of sexually transmissible infections (STIs) and blood-borne viruses (BBVs). However, there has been no sustained effort to monitor the legal environment surrounding STIs and BBVs. This article presents the first data on the incidence and impacts of unmet legal needs for those affected by an STI or BBV in Australia using a survey administered to a sample of the Australian sexual health and BBV workforce. Migration, Housing, Money/Debt, Health (including complaints about health services), and Crime (accused/offender) were reported as the five most common legal need areas, with 60% of respondents describing these legal problems as generating a 'severe' impact on health. These results indicate that unmet legal needs generate significant negative impacts in terms of individual health, on public health, and the ability to provide sustainable services such as testing and treatment to those facing unmet legal needs.

Chaaya, R, Steele, JR, Oliver, BG, Chen, H & Machaalani, R 2023, 'Effects of e-vapour and high-fat diet on the immunohistochemical staining of nicotinic acetylcholine receptors, apoptosis, microglia and astrocytes in the adult male mouse hippocampus', Journal of Chemical Neuroanatomy, vol. 132, pp. 102303-102303.
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The use of e-cigarettes/e-vapour, and the consumption of a high-fat diet (HFD), are two popular lifestyle choices associated with alterations in the hippocampus. This study, using a mouse model, investigated the effects of exposure to e-vapour (± nicotine) and HFD (43% fat) consumption, on the expression of nicotinic acetylcholine receptor (nAChR) subunits α3, α4, α7 and β2, apoptosis markers caspase-3 and TUNEL, microglial marker Iba-1, and astrocyte marker GFAP, in hippocampal subregions of dentate gyrus (DG) and cornu ammonis (CA) 1-3. The major findings included: (1) HFD alone had minimal effect with no consistent pattern or interaction between the markers, (2) E-vapour (± nicotine) predominantly affected the CA2 subregion, decreasing α7 and β2 nAChR subunits and Iba-1, (3) Nicotine e-vapour increased TUNEL across all subregions, and (4) HFD, in the presence of nicotine-free e-vapour, decreased caspase-3 and increased TUNEL across all regions, and decreased Iba-1 in the CA subregions, while HFD and nicotine-containing e-vapour, subregion specifically affected the α3, α4 and α7 nAChR subunits, with a protective effect against change in GFAP in the DG and Iba-1 in the CA1 and CA3. These findings highlight that e-vapour itself alters nAChRs, particularly in the CA2 subregion, associated with a decrease in neuroinflammatory response (Iba-1) across the whole hippocampus, and the addition of nicotine increases cell apoptosis across the whole hippocampus. HFD alone was not detrimental in our model, but in the presence of nicotine-free e-vapour, it differentially affected apoptosis, while the addition of nicotine increased nAChR subunits.

Chakraborty, A, Paudel, KR, Wang, C, De Rubis, G, Chellappan, DK, Hansbro, PM, Samuel, CS & Dua, K 2023, 'Anti-inflammatory and anti-fibrotic effects of berberine-loaded liquid crystalline nanoparticles.', EXCLI J, vol. 22, pp. 1104-1108.
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Champion, C, Lawson, JR, Pardoe, J, Cruz, DO, Fowler, AM, Jaine, F, Schilling, HT & Coleman, MA 2023, 'Multi-criteria analysis for rapid vulnerability assessment of marine species to climate change', Climatic Change, vol. 176, no. 8.
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AbstractThe accelerating pace of climate-induced stress to global ecosystems threatens the sustainable management and conservation of biodiversity. To effectively respond, researchers and managers require rapid vulnerability assessment tools that can be readily implemented using diverse and existing knowledge sources. Here we demonstrate the application of multi-criteria analysis (MCA) for this purpose using a group of coastal-pelagic fishes from south-eastern Australia as a case-study. We show that MCA has the capacity to formally structure diverse knowledge sources, ranging from peer-reviewed information (which informed 29.2% of criteria among models) to expert knowledge (which informed 22.6% of criteria among models), to quantify the sensitivity of species to biophysical conditions. By integrating MCA models with spatial climate data over historical and future periods, we demonstrate the application of MCA for rapidly assessing the vulnerability of marine species to climate change. Spatial analyses revealed an apparent trend among case-study species towards increasing or stable vulnerability to projected climate change throughout the northern (i.e. equatorward) extent of the study domain and the emergence of climate refugia throughout southern (i.e. poleward) regions. Results from projections using the MCA method were consistent with past analyses of the redistribution of suitable habitat for coastal-pelagic fishes off eastern Australia under climate change. By demonstrating the value of MCA for rapidly assessing the vulnerability of marine species to climate change, we highlight the opportunity to develop user-friendly software infrastructures integrated with marine climate projection data to support the interdisciplinary application of this method.

Chan, Y, Raju Allam, VSR, Paudel, KR, Singh, SK, Gulati, M, Dhanasekaran, M, Gupta, PK, Jha, NK, Devkota, HP, Gupta, G, Hansbro, PM, Oliver, BGG, Chellappan, DK & Dua, K 2023, 'Nutraceuticals: unlocking newer paradigms in the mitigation of inflammatory lung diseases', Critical Reviews in Food Science and Nutrition, vol. 63, no. 19, pp. 3302-3332.
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Chau, K, Fleck, R, Irga, PJ, Torpy, FR, Wilkinson, SJ & Castel, A 2023, 'Hempcrete as a substrate for fungal growth under high humidity and variable temperature conditions', Construction and Building Materials, vol. 398, pp. 132373-132373.
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Bio-based alternatives for existing construction materials can be used to reduce the carbon footprint of the built environment. Hempcrete is one of these materials and is both an excellent hygric/thermal regulator and is carbon negative. However, this novel material is still incompletely researched, especially its fungal growth potential specifically within warm and humid environments. The incorporation of significant biological material within hempcrete can enable it to act as a microbial growth medium, with the corresponding potential for the release of bioaerosols. The aim of this research was thus to investigate the overall practicality of hempcrete implementation in a humid climate. To achieve this, the endogenous fungal genera on a sample of hempcrete were identified, fungal propagules aerosolized from a hempcrete sample enumerated, and a range of temperatures tested to determine their effect on fungi growth determined. Trials were performed to determine whether hempcrete can be effectively decontaminated with common materials to manage microbial growth. Under high humidity, fungal propagule emissions were high with low diversity, with potentially allergenic fungi detected. Disinfection of high fungal load hempcrete samples was able to reduce ∼94% of the fungal observations and reduce aerosolized counts to average background tropical fungal counts. The range of temperatures tested were not found to effect fungal growth, contrary to the consensus of the literature. Overall, these properties make hempcrete suited to humid areas, however, further research to investigate the potential effects of fungi on the material remains lacking.

Chen, H, Kimyon, O, Chen, R, Gunawan, C, Ramandi, HL, Canbulat, I & Saydam, S 2023, 'The effectiveness of epoxy coating for preventing microbially induced corrosion of rock bolts', IOP Conference Series: Earth and Environmental Science, vol. 1124, no. 1, pp. 012097-012097.
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Abstract In the past two decades, the corrosion failures of rock reinforcement bolts in underground coal mines have been increasingly reported. Preliminary studies have shown that these failures were predominantly related to pitting and stress corrosion cracking. The analyses in affected mines indicated microbially induced corrosion (MIC) as one of the primary corrosion causes. As such, there is an urgent demand from industries to develop methods to mitigate MIC-associated failures of rock bolts in underground coal mines. This study examined epoxy coating to determine its effectiveness in preventing biofilm formation on steel surfaces and, in turn, averting MIC. The corrosion-causing bacteria were isolated and enriched from groundwater samples collected from the affected mine sites. Coated and uncoated rock bolt samples were prepared from the bolts and incubated in media in the absence and presence of the corrosion-causing bacteria. Fluorescence microscopy imaging found no evidence of bacterial biomass growth on the surface of the epoxy-coated steel surfaces after 30 days, while the non-coated surfaces were colonised by biomass. The observations suggest the potential of epoxy coating for bolt MIC prevention. Future studies to assess the applicability of epoxy coating in the underground mine environment are recommended.

Chen, H, Yang, Y, Odisho, D, Wu, S, Yi, C & Oliver, BG 2023, 'Can biomarkers be used to diagnose attention deficit hyperactivity disorder?', Frontiers in Psychiatry, vol. 14, p. 1026616.
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Currently, the diagnosis of attention deficit hyperactivity disorder (ADHD) is solely based on behavioral tests prescribed by the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition (DSM-5). However, biomarkers can be more objective and accurate for diagnosis and evaluating treatment efficacy. Thus, this review aimed to identify potential biomarkers for ADHD. Search terms “ADHD,” and “biomarker” combined with one of “protein,” “blood/serum,” “gene,” and “neuro” were used to identify human and animal studies in PubMed, Ovid Medline, and Web of Science. Only papers in English were included. Potential biomarkers were categorized into radiographic, molecular, physiologic, or histologic markers. The radiographic analysis can identify specific activity changes in several brain regions in individuals with ADHD. Several molecular biomarkers in peripheral blood cells and some physiologic biomarkers were found in a small number of participants. There were no published histologic biomarkers for ADHD. Overall, most associations between ADHD and potential biomarkers were properly controlled. In conclusion, a series of biomarkers in the literature are promising as objective parameters to more accurately diagnose ADHD, especially in those with comorbidities that prevent the use of DSM-5. However, more research is needed to confirm the reliability of the biomarkers in larger cohort studies.

Chen, X, Yang, H, Gu, Y, Wen, C, Sun, Y, Ke, J & Feng, W 2023, 'Interparticle energy transfer between NaNdF4 and NaYbF4 in self-assembled nanostructures', Journal of Rare Earths.
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Chen, Y, Gale, A, Yamamura, K, Horder, J, Condos, A, Watanabe, K, Taniguchi, T, Toth, M & Aharonovich, I 2023, 'Annealing of blue quantum emitters in carbon-doped hexagonal boron nitride', Applied Physics Letters, vol. 123, no. 4.
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Reliable methods to create quantum emitters in hexagonal boron nitride (hBN) are highly sought after for scalable applications in quantum photonic devices. Specifically, recent efforts have focused on defects in hBN with a zero phonon line at 2.8 eV (436 nm). Here, we employ carbon-doped hBN crystals that were irradiated by an electron beam to generate these emitters and perform annealing treatments to investigate the stability of the emitters. We find that the blue emitters are stable up to ∼800 °C. However, upon annealing to 1000 °C, the emitters disappear, and a family of other emitters appears in the region of hBN that had been irradiated by an electron beam. Our findings contribute to the understanding of emitter species and emitter formation in hBN.

Chen, Y, Li, C, Yang, T, Ekimov, EA, Bradac, C, Ha, ST, Toth, M, Aharonovich, I & Tran, TT 2023, 'Real-Time Ratiometric Optical Nanoscale Thermometry', ACS Nano, vol. 17, no. 3, pp. 2725-2736.
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Chen, Y, White, S, Ekimov, EA, Bradac, C, Toth, M, Aharonovich, I & Tran, TT 2023, 'Ultralow-Power Cryogenic Thermometry Based on Optical-Transition Broadening of a Two-Level System in Diamond', ACS Photonics, vol. 10, no. 8, pp. 2481-2487.
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Cryogenic temperatures are the prerequisite for many advanced scientific applications and technologies. The accurate determination of temperature in this range and at the submicrometer scale is, however, nontrivial. This is due to the fact that temperature reading in cryogenic conditions can be inaccurate due to optically induced heating. Here, we present an ultralow-power, optical thermometry technique that operates at cryogenic temperatures. The technique exploits the temperature-dependent linewidth broadening measured by resonant photoluminescence of a two-level system: a germanium-vacancy color center in a nanodiamond host. The proposed technique achieves a relative sensitivity of ∼20% K-1, at 5 K. This is higher than any other all-optical nanothermometry method. Additionally, it achieves such sensitivities while employing excitation powers of just a few tens of nanowatts, several orders of magnitude lower than other traditional optical thermometry protocols. To showcase the performance of the method, we demonstrate its ability to accurately read out local differences in temperatures at various target locations of a custom-made microcircuit. Our work is a step toward the advancement of nanoscale optical thermometry at cryogenic temperatures.

Chhor, M, Law, W, Pavlovic, M, Aksentijevic, D, McGrath, K & McClements, L 2023, 'Diagnostic and prognostic biomarkers reflective of cardiac remodelling in diabetes mellitus: A scoping review', Diabetic Medicine, vol. 40, no. 5.
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AbstractAimsThe aim of this scoping review is to evaluate the current biomarkers used in the assessment of adverse cardiac remodelling in people with diabetes mellitus (DM) and in the diagnosis and prognosis of subsequent cardiovascular disease. We aim to discuss the biomarkers' pathophysiological roles as a reflection of the cardiac remodelling mechanisms in the presence of DM.MethodsWe performed the literature search to include studies from 2003 to 2021 using the following databases: MEDLINE, Scopus, Web of Science, PubMed, and Cochrane library. Articles that met our inclusion criteria were screened and appraised before being included in this review. The PRISMA guidelines for Scoping Reviews were followed.ResultsOur literature search identified a total of 43 eligible articles, which were included in this scoping review. We identified 15 different biomarkers, each described by at least two studies, that were used to determine signs of cardiac remodelling in cardiovascular disease (CVD) and people with DM. NT‐proBNP was identified as the most frequently employed biomarker in this context; however, we also identified emerging biomarkers including hs‐CRP, hs‐cTnT, and Galectin‐3.ConclusionThere is a complex relationship between DM and cardiovascular health, where more research is needed. Current biomarkers reflective of adverse cardiac remodelling in DM are often used to diagnose other CVDs, such as NT‐proBNP for heart failure. Hence there is a need for identification of specific biomarkers that can detect early signs of cardiac remodelling in the presence of DM. Further research into these biomarkers and mechanisms can deepen our understanding of their role in DM‐associated CVD and lead to better preve...

Clain, C, Stewart, J, Fowler, A & Diamond, S 2023, 'Age, growth and length-to-weight relationship of largehead hairtail (Trichiurus lepturus) in south-eastern Australia suggest a distinct population', Aquaculture and Fisheries.
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The age, growth rates and length to weight relationships for the south-eastern Australian population of largehead hairtail (Trichiurus lepturus) were investigated for the first time. Age was estimated by counting annuli in sectioned sagittal otoliths, with a maximum age of 8 years estimated for males and females. We found no significant differences in the growth rates of males and females over the size (12–78 cm pre-anal length (PL)) and age (0–8 years) ranges sampled. However, females in our collection were larger on average than males, and all fish sampled >60 cm PL were female, suggesting that females may grow to larger sizes than males and that sampling of greater numbers of larger and older fish may be required in future. T. lepturus growth was described by the von Bertalanffy growth function parameters L∝ = 74.89 cm PL, K = 0.13yr−1 and t0 = −0.80 yr, with the L∝ being amongst the largest reported for the species. Growth was variable, with the sizes at any given age spanning up to 50 cm PL. Female T. lepturus increased in body weight relative to length faster than males, as has been reported in other populations. The length/weight relationship for the south-eastern Australian population was significantly different, with almost no overlap, from that reported for T. lepturus in the Arabian Sea. The substantial differences in growth rates, maximum sizes and body morphometrics of T. lepturus from south-eastern Australia in comparison to other populations globally are consistent with the hypotheses that it represents a distinct population, although investigations using additional population markers are required to verify this.

Clain, C, Stewart, J, Fowler, A & Diamond, S 2023, 'Reproductive biology of largehead hairtail (Trichiurus lepturus) in south-eastern Australia', Aquaculture and Fisheries, vol. 8, no. 2, pp. 148-158.
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Knowledge of reproductive biology and life-history traits of populations exploited by fisheries is important for their sustainable management. We investigated the life-history traits of Trichiurus lepturus (largehead hairtail) in south-eastern Australia; a region of low exploitation for this otherwise heavily exploited circumglobal species, to investigate whether there were differences in the reproductive biology and life-history traits in the south-east Australian population compared with those in other regions. We also used histological sections to examine male and female gonads at a microscopic level. Trichiurus lepturus in south-eastern Australia had a greater maximum length (193 cm total length (TL)), matured at a larger length (108 cm TL at 50% mature) and had a spawning period (March to September, Austral winter) that was inconsistent with other regions. The overall sex ratio of 1:0.4 females: males was consistent with a female dominant sex ratio observed in other regions, particularly in larger length classes. However, females in the current study dominated samples from both estuarine and coastal habitats, as well as during the spawning and non-spawning periods, which is not consistent with the patterns found in other regions. Differences in south-eastern Australia may relate to limited fishing pressure, genetic variation, or differences in environmental factors that influence reproductive development, including temperature, trophic resources and habitat.

Clarke, RJ, Lev, B, Chennath, M, Allen, TW, Cranfield, CG, Blayney, E-L & Cornelius, F 2023, 'Involvement of alpha-subunit N-termini in the mechanism and regulation of the Na+,K+- and H+,K+-ATPases', Biophysical Journal, vol. 122, no. 3, pp. 529a-529a.
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Clerc, EE, Raina, J-B, Keegstra, JM, Landry, Z, Pontrelli, S, Alcolombri, U, Lambert, BS, Anelli, V, Vincent, F, Masdeu-Navarro, M, Sichert, A, De Schaetzen, F, Sauer, U, Simó, R, Hehemann, J-H, Vardi, A, Seymour, JR & Stocker, R 2023, 'Strong chemotaxis by marine bacteria towards polysaccharides is enhanced by the abundant organosulfur compound DMSP', Nature Communications, vol. 14, no. 1, p. 8080.
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AbstractThe ability of marine bacteria to direct their movement in response to chemical gradients influences inter-species interactions, nutrient turnover, and ecosystem productivity. While many bacteria are chemotactic towards small metabolites, marine organic matter is predominantly composed of large molecules and polymers. Yet, the signalling role of these large molecules is largely unknown. Using in situ and laboratory-based chemotaxis assays, we show that marine bacteria are strongly attracted to the abundant algal polysaccharides laminarin and alginate. Unexpectedly, these polysaccharides elicited stronger chemoattraction than their oligo- and monosaccharide constituents. Furthermore, chemotaxis towards laminarin was strongly enhanced by dimethylsulfoniopropionate (DMSP), another ubiquitous algal-derived metabolite. Our results indicate that DMSP acts as a methyl donor for marine bacteria, increasing their gradient detection capacity and facilitating their access to polysaccharide patches. We demonstrate that marine bacteria are capable of strong chemotaxis towards large soluble polysaccharides and uncover a new ecological role for DMSP in enhancing this attraction. These navigation behaviours may contribute to the rapid turnover of polymers in the ocean, with important consequences for marine carbon cycling.

Clover Ree, L, Chadwick, S & Moret, S 2023, 'Comparison of carbon and iron oxide based powder suspension formulations', Forensic Science International, vol. 347, pp. 111685-111685.
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Colarusso, C, Terlizzi, M, Falanga, A, Stathopoulos, G, De Lucia, L, Hansbro, PM, Pinto, A & Sorrentino, R 2023, 'Absent in melanoma 2 (AIM2) positive profile identifies a poor prognosis of lung adenocarcinoma patients', International Immunopharmacology, vol. 124, pp. 110990-110990.
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Collins, S, Maestrini, L, Hui, FKC, Stuart, B & Ueland, M 2023, 'The use of generalized linear mixed models to investigate postmortem lipids in textiles', iScience, vol. 26, no. 8, pp. 107371-107371.
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Collins, S, Stuart, B & Ueland, M 2023, 'Anatomical location dependence of human decomposition products in clothing', Australian Journal of Forensic Sciences, vol. 55, no. 3, pp. 363-375.
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The human decomposition process results in the formation of particular biological compounds, the chemistry of which provides valuable insight into the nature of a death. This paper reports the findings of a study of the decomposition process of clothed human remains at the Australian Facility for Taphonomic Experimental Research (AFTER). An investigation into how decomposition products appear in opposing anatomical regions, namely the anterior and posterior regions of the body, has been carried out. The chemistry of the lipid and protein components and their by-products formed in the first months of decomposition were examined using infrared spectroscopy. The study has demonstrated a clear difference in the pattern of formation of human decomposition products absorbed by textiles located in the anterior versus posterior regions. The time of appearance of established compounds at recognized stages of human decomposition varies notably depending on the anatomical location of the clothing.

Collins, S, Stuart, B & Ueland, M 2023, 'The use of lipids from textiles as soft-tissue biomarkers of human decomposition', Forensic Science International, vol. 343, pp. 111547-111547.
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The ability to determine the post-mortem interval (PMI) in complex death investigations involving human remains, is a vital task faced by law enforcement. Establishing the PMI in a case can significantly aid in the reconstruction of forensically relevant events surrounding that death. However, due to the complexities surrounding the decomposition of human remains, the determination of the PMI still remains a challenge in some cases. Thus, the identification of biomarkers of human decomposition are an emerging, and essential, area of research. Previous studies have also demonstrated great success in the use of textiles as a host to indirectly capture decomposition by-products. This study reports the successful adaptation and optimisation of an analytical chemical workflow for the targeted analysis of lipids from textiles associated with decomposing human remains using gas-chromatography (GC) coupled with tandem mass spectrometry (MS/MS). This study discusses novel information regarding the complex challenges of matrix effects observed with decomposition samples. In addition, the first lipid profiles obtained from textiles associated with two decomposing human donors from the Australian Facility for Taphonomic Experimental Research (AFTER) using GC-MS/MS are presented.

Cooper, GE, Mayall, J, Donovan, C, Haw, TJ, Budden, KF, Hansbro, NG, Blomme, EE, Maes, T, Kong, CW, Horvat, JC, Khakoo, SI, Wilkinson, TMA, Hansbro, PM & Staples, KJ 2023, 'Antiviral Responses of Tissue-resident CD49a⁺ Lung Natural Killer Cells Are Dysregulated in Chronic Obstructive Pulmonary Disease', American Journal of Respiratory and Critical Care Medicine, vol. 207, no. 5, pp. 553-565.
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RATIONALE: Tissue-resident natural killer cells have been identified in numerous organs, but little is known about their functional contribution to respiratory immunity, in particular during chronic lung diseases such as COPD. OBJECTIVES: To investigate the phenotype and antiviral responses of trNK cells in murine cigarette smoke-induced experimental COPD and in human lung parenchyma from COPD donors. METHODS: Mice were exposed to cigarette smoke for 10 weeks to induce COPD-like lung disease. Lung tissue resident NK cell phenotypes and function were analysed by flow cytometry in both murine and human disease with and without challenge with influenza A virus. MEASUREMENTS AND MAIN RESULTS: In the mouse lung CD49a+CD49b+EOMES+ and CD49a+CD49b-EOMESlo NK cell populations had a distinct phenotype compared with CD49a- circulating NK cells. CD49a+ NK cells were more extensively altered earlier in disease onset than circulating NK cells and increased proportions of CD49a+ NK cells correlated with worsening disease in both murine and human COPD. Furthermore, the presence of lung disease delayed both circulating and tissue-resident NK cell functional responses to influenza infection. CD49a+ NK cells markedly increased their NKG2D, CD103 and CD69 expression in experimental COPD following influenza infection, and human CD49a+ NK cells were hyperactive to ex vivo influenza infection in COPD donors. CONCLUSIONS: Collectively, these results demonstrate that tissue-resident NK cell function is altered in cigarette smoke-induced disease and suggests that smoke exposure may aberrantly prime tissue-resident NK cell responsiveness to viral infection. This may contribute to excess inflammation during viral exacerbations of COPD.

Courtney Jones, SK, Geange, SR, Hanea, A, Camac, J, Hemming, V, Doobov, B, Leigh, A & Nicotra, AB 2023, 'IDEAcology: An interface to streamline and facilitate efficient, rigorous expert elicitation in ecology', Methods in Ecology and Evolution, vol. 14, no. 8, pp. 2019-2028.
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AbstractHere, we demonstrate how IDEAcology aids in preparing for and implementing a structured expert elicitation using the IDEA protocol, an iterative quantitative expert elicitation framework.Expert judgement is used to inform decision‐making on environmental assessment and management when imminent decisions are required, and quantitative data are absent or uninformative. Structured elicitation protocols can help improve the final judgements derived from experts, but they can also be administratively heavy and time‐consuming, requiring manual collation of experts' estimates and rationales, construction and dissemination of summary plots for discussion and collating final estimates post‐discussion. These challenges highlight the need for a centralised portal that enables synchronous access by all contributors, real‐time structured facilitation of discussion, whether in person or online, and streamlined data management.To meet this need, we developed the IDEAcology interface (www.ideacology.com) to support data collation, summary, interactions and ultimately the deployment of structured expert elicitation using the IDEA protocol. The IDEAcology interface is designed to be a central portal for scientists and practitioners to easily implement structured expert elicitation projects, while also facilitating data management by providing a reliable and efficient way for elicitation managers to design and run an elicitation, and for experts to input, visualise and cross‐examine estimates.The key advantages that IDEAcology provides include an easy‐to‐use interface with synchronous access to a single platform, reducing logistic diffic...

Cowan, AE, Jun, S, Tooze, JA, Dodd, KW, Gahche, JJ, Eicher-Miller, HA, Guenther, PM, Dwyer, JT, Potischman, N, Bhadra, A, Carroll, RJ & Bailey, RL 2023, 'A narrative review of nutrient based indexes to assess diet quality and the proposed total nutrient index that reflects total dietary exposures', Critical Reviews in Food Science and Nutrition, vol. 63, no. 12, pp. 1722-1732.
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A priori dietary indices provide a standardized, reproducible way to evaluate adherence to dietary recommendations across different populations. Existing nutrient-based indices were developed to reflect food/beverage intake; however, given the high prevalence of dietary supplement (DS) use and its potentially large contribution to nutrient intakes for those that use them, exposure classification without accounting for DS is incomplete. The purpose of this article is to review existing nutrient-based indices and describe the development of the Total Nutrient Index (TNI), an index developed to capture usual intakes from all sources of under-consumed micronutrients among the U.S. population. The TNI assesses U.S. adults' total nutrient intakes relative to recommended nutrient standards for eight under-consumed micronutrients identified by the Dietary Guidelines for Americans: calcium, magnesium, potassium, choline, and vitamins A, C, D, E. The TNI is scored from 0 to 100 (truncated at 100). The mean TNI score of U.S. adults (≥19 y; n = 9,954) based on dietary data from NHANES 2011-2014, was 75.4; the mean score for the index ignoring DS contributions was only 69.0 (t-test; p < 0.001). The TNI extends existing measures of diet quality by including nutrient intakes from all sources and was developed for research, monitoring, and policy purposes.

Cui, G, Konciute, MK, Ling, L, Esau, L, Raina, J-B, Han, B, Salazar, OR, Presnell, JS, Rädecker, N, Zhong, H, Menzies, J, Cleves, PA, Liew, YJ, Krediet, CJ, Sawiccy, V, Cziesielski, MJ, Guagliardo, P, Bougoure, J, Pernice, M, Hirt, H, Voolstra, CR, Weis, VM, Pringle, JR & Aranda, M 2023, 'Molecular insights into the Darwin paradox of coral reefs from the sea anemone Aiptasia', Science Advances, vol. 9, no. 11.
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Symbiotic cnidarians such as corals and anemones form highly productive and biodiverse coral reef ecosystems in nutrient-poor ocean environments, a phenomenon known as Darwin’s paradox. Resolving this paradox requires elucidating the molecular bases of efficient nutrient distribution and recycling in the cnidarian-dinoflagellate symbiosis. Using the sea anemone Aiptasia, we show that during symbiosis, the increased availability of glucose and the presence of the algae jointly induce the coordinated up-regulation and relocalization of glucose and ammonium transporters. These molecular responses are critical to support symbiont functioning and organism-wide nitrogen assimilation through glutamine synthetase/glutamate synthase–mediated amino acid biosynthesis. Our results reveal crucial aspects of the molecular mechanisms underlying nitrogen conservation and recycling in these organisms that allow them to thrive in the nitrogen-poor ocean environments.

Cummins, ML, Li, D, Ahmad, A, Bushell, R, Noormohammadi, AH, Wijesurendra, DS, Stent, A, Marenda, MS & Djordjevic, SP 2023, 'Whole Genome Sequencing of Avian Pathogenic Escherichia coli Causing Bacterial Chondronecrosis and Osteomyelitis in Australian Poultry', Microorganisms, vol. 11, no. 6, pp. 1513-1513.
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Bacterial chondronecrosis with osteomyelitis (BCO) impacts animal welfare and productivity in the poultry industry worldwide, yet it has an understudied pathogenesis. While Avian Pathogenic Escherichia coli (APEC) are known to be one of the main causes, there is a lack of whole genome sequence data, with only a few BCO-associated APEC (APECBCO) genomes available in public databases. In this study, we conducted an analysis of 205 APECBCO genome sequences to generate new baseline phylogenomic knowledge regarding the diversity of E. coli sequence types and the presence of virulence associated genes (VAGs). Our findings revealed the following: (i) APECBCO are phylogenetically and genotypically similar to APEC that cause colibacillosis (APECcolibac), with globally disseminated APEC sequence types ST117, ST57, ST69, and ST95 being predominate; (ii) APECBCO are frequent carriers of ColV-like plasmids that carry a similar set of VAGs as those found in APECcolibac. Additionally, we performed genomic comparisons, including a genome-wide association study, with a complementary collection of geotemporally-matched genomes of APEC from multiple cases of colibacillosis (APECcolibac). Our genome-wide association study found no evidence of novel virulence loci unique to APECBCO. Overall, our data indicate that APECBCO and APECcolibac are not distinct subpopulations of APEC. Our publication of these genomes substantially increases the available collection of APECBCO genomes and provides insights for the management and treatment strategies of lameness in poultry.

Dahal, A, McNevin, D, Chikhani, M & Ward, J 2023, 'An interdisciplinary forensic approach for human remains identification and missing persons investigations', WIREs Forensic Science, vol. 5, no. 4.
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AbstractThe resolution of unidentified human remains (UHR) and long‐term missing persons (LTMP) cases is paramount for administrative, legal, and humanitarian reasons. There are various forensic profiling methods for human identification; however, their utility is dependent on several factors. First, UHR can be found in different stages of decomposition, so the availability and diversity of post‐mortem (PM) information will differ. Second, the availability and totality of the LTMP's ante‐mortem (AM) information will differ. Therefore, the suitability of existing methods will be dependent on the quality and quantity of PM and/or AM data available for comparison. Visual recognition is the simplest and quickest method, but typically not practiced or possible, owing to the altered, fragmented, or skeletonized state of UHR. Primary forensic profiling methods involve the comparison of fingerprint, dental, DNA, and medical data. Secondary forensic profiling methods from anthropology, radiology, geochemistry, and anatomy disciplines can provide supplementary evidence to support comparative identification approaches. Emerging forensic molecular technologies such as genomics, microbiomics, epigenetics, and proteomics, together with individual digital footprints from personal devices, offer new investigative leads for establishing identity. However, despite the success of these individual methods, their limitations must be considered when used in isolation. Through the development of a guiding forensic examination framework, this review endorses an interdisciplinary response to unidentified and missing persons investigations, where various forensic specialists collaboratively examine UHR using a suite of contemporary forensic profiling methods to produce multiple and/or different lines of evidence to link them effectively, efficiently, comprehensively, and systematically to LTMP.This article is categorized under:

Dai, G, Ma, Y, Hasler, J, Chen, J & Carroll, RJ 2023, 'A Robust Approach for Electronic Health Record–Based Case-Control Studies with Contaminated Case Pools', Biometrics, vol. 79, no. 3, pp. 2023-2035.
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Abstract We consider analyses of case-control studies assembled from electronic health records (EHRs) where the pool of cases is contaminated by patients who are ineligible for the study. These ineligible patients, referred to as “false cases,” should be excluded from the analyses if known. However, the true outcome status of a patient in the case pool is unknown except in a subset whose size may be arbitrarily small compared to the entire pool. To effectively remove the influence of the false cases on estimating odds ratio parameters defined by a working association model of the logistic form, we propose a general strategy to adaptively impute the unknown case status without requiring a correct phenotyping model to help discern the true and false case statuses. Our method estimates the target parameters as the solution to a set of unbiased estimating equations constructed using all available data. It outperforms existing methods by achieving robustness to mismodeling the relationship between the outcome status and covariates of interest, as well as improved estimation efficiency. We further show that our estimator is root-n-consistent and asymptotically normal. Through extensive simulation studies and analysis of real EHR data, we demonstrate that our method has desirable robustness to possible misspecification of both the association and phenotyping models, along with statistical efficiency superior to the competitors.

Dang, K, Ryan, LM, Akkaya Hocagil, T, Cook, RJ, Richardson, GA, Day, NL, Coles, CD, Carmichael Olson, H, Jacobson, SW & Jacobson, JL 2023, 'Bayesian modelling of effects of prenatal alcohol exposure on child cognition based on data from multiple cohorts', Australian & New Zealand Journal of Statistics, vol. 65, no. 3, pp. 167-186.
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SummaryHigh levels of prenatal alcohol exposure (PAE) result in significant cognitive deficits in children, but the exact nature of the dose‐response relationship is less well understood. To investigate this relationship, data were assembled from six longitudinal birth cohort studies examining the effects of PAE on cognitive outcomes from early school age through adolescence. Structural equation models (SEMs) are a natural approach to consider, because of the way they conceptualise multiple observed outcomes as relating to an underlying latent variable of interest, which can then be modelled as a function of exposure and other predictors of interest. However, conventional SEMs could not be fitted in this context because slightly different outcome measures were used in the six studies. In this paper we propose a multi‐group Bayesian SEM that maps the unobserved cognition variable to a broad range of observed outcomes. The relation between these variables and PAE is then examined while controlling for potential confounders via propensity score adjustment. By examining different possible dose‐response functions, the proposed framework is used to investigate whether there is a threshold PAE level that results in minimal cognitive deficit.

Dang, K, Ryan, LM, Cook, RJ, Akkaya Hocagil, T, Jacobson, SW & Jacobson, JL 2023, 'Bayesian outcome selection modeling', Stat, vol. 12, no. 1.
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In psychiatric and social epidemiology studies, it is common to measure multiple different outcomes using a comprehensive battery of tests thought to be related to an underlying construct of interest. In the research that motivates our work, researchers wanted to assess the impact of in utero alcohol exposure on child cognition and neuropsychological development, which are evaluated using a range of different psychometric tests. Statistical analysis of the resulting multiple outcomes data can be challenging, because the outcomes measured on the same individual are not independent. Moreover, it is unclear, a priori, which outcomes are impacted by the exposure under study. While researchers will typically have some hypotheses about which outcomes are important, a framework is needed to help identify outcomes that are sensitive to the exposure and to quantify the associated treatment or exposure effects of interest. We propose such a framework using a modification of stochastic search variable selection, a popular Bayesian variable selection model and use it to quantify an overall effect of the exposure on the affected outcomes. The performance of the method is investigated empirically and an illustration is given through application using data from our motivating study.

Daniels, RK, Arnold, MD, Heywood, ZE, Mallinson, JB, Bones, PJ & Brown, SA 2023, 'Brainlike Networks of Nanowires and Nanoparticles: A Change of Perspective', Physical Review Applied, vol. 20, no. 3.
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The connectivity of self-assembled networks of nanowires and nanoparticles is believed to strongly influence their performance in brainlike (neuromorphic) computing applications. Here we present a new perspective on the connectivity of these networks in which their neuronlike active elements are viewed in the same way as the nodes in artificial and biological neuronal networks. We consider two-dimensional and quasi-three-dimensional networks of nanowires and percolating networks of nanoparticles and show that, from this new perspective, they all have similar small-world characteristics. Other characteristics which may impact the computational performance of the networks are also investigated, including their assortativity and the scalefree nature of the nanoparticle networks. Taken together, these results allow comparison of key network characteristics for a variety of self-assembled nanoscale networks, and provide a basis for detailed investigations of computational performance.

Datsyuk, JK, Paudel, KR, Rajput, R, Kokkinis, S, El Sherkawi, T, Singh, SK, Gupta, G, Chellappan, DK, Yeung, S, Hansbro, PM, Oliver, BGG, Santos, HA, Dua, K & De Rubis, G 2023, 'Emerging applications and prospects of NFκB decoy oligodeoxynucleotides in managing respiratory diseases', Chemico-Biological Interactions, vol. 385, pp. 110737-110737.
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Davila, Y & Cabral, L 2023, 'Science Extension – Critical Analysis of Scientific Articles', Science Education News, vol. 72, no. 3.
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This article outlines strategies to teach students how to conduct “Critical Analysis” of scientific articles for the HSC Science Extension course, based on a recent article titled: Embedding Scaffolded Reading Practices into the First-Year University Science Curriculum (Griffiths and Davila 2022). Strategies outlined in this article were modified for Year 12 Science Extension students.

De Rubis, G, Paudel, KR, Corrie, L, Mehndiratta, S, Patel, VK, Kumbhar, PS, Manjappa, AS, Disouza, J, Patravale, V, Gupta, G, Manandhar, B, Rajput, R, Robinson, AK, Reyes, R-J, Chakraborty, A, Chellappan, DK, Singh, SK, Oliver, BGG, Hansbro, PM & Dua, K 2023, 'Applications and advancements of nanoparticle-based drug delivery in alleviating lung cancer and chronic obstructive pulmonary disease', Naunyn-Schmiedeberg's Archives of Pharmacology.
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Lung cancer (LC) and chronic obstructive pulmonary disease (COPD) are among the leading causes of mortality worldwide. Cigarette smoking is among the main aetiologic factors for both ailments. These diseases share common pathogenetic mechanisms including inflammation, oxidative stress, and tissue remodelling. Current therapeutic approaches are limited by low efficacy and adverse effects. Consequentially, LC has a 5-year survival of < 20%, while COPD is incurable, underlining the necessity for innovative treatment strategies. Two promising emerging classes of therapy against these diseases include plant-derived molecules (phytoceuticals) and nucleic acid-based therapies. The clinical application of both is limited by issues including poor solubility, poor permeability, and, in the case of nucleic acids, susceptibility to enzymatic degradation, large size, and electrostatic charge density. Nanoparticle-based advanced drug delivery systems are currently being explored as flexible systems allowing to overcome these limitations. In this review, an updated summary of the most recent studies using nanoparticle-based advanced drug delivery systems to improve the delivery of nucleic acids and phytoceuticals for the treatment of LC and COPD is provided. This review highlights the enormous relevance of these delivery systems as tools that are set to facilitate the clinical application of novel categories of therapeutics with poor pharmacokinetic properties. This picture was generated with BioRender.

De Rubis, G, Paudel, KR, Liu, G, Agarwal, V, MacLoughlin, R, de Jesus Andreoli Pinto, T, Singh, SK, Adams, J, Nammi, S, Chellappan, DK, Oliver, BGG, Hansbro, PM & Dua, K 2023, 'Berberine-loaded engineered nanoparticles attenuate TGF-β-induced remodelling in human bronchial epithelial cells', Toxicology in Vitro, vol. 92, pp. 105660-105660.
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Deignan, LK, Pwa, KH, Loh, AAR, Rice, SA & McDougald, D 2023, 'The microbiomes of two Singaporean corals show site-specific differentiation and variability that correlates with the seasonal monsoons', Coral Reefs, vol. 42, no. 3, pp. 677-691.
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AbstractCorals host abundant microbial communities, or microbiomes, that play essential roles in the function of the coral holobiont. We examined the mucus microbiome in corals within the port of Singapore, where corals persist despite intense anthropogenic impacts. The coral mucus microbiomes of Pectinia paeonia and Platygyra sinensis at three reef sites were tracked by 16S rRNA gene amplicon sequencing from January 2019 to January 2020. Both coral species displayed spatial and temporal differences in microbiome composition, suggesting site specificity and seasonality in microbiome composition consistent with the monsoons. The temporal shifts in relative abundance of dominant taxa were different between the two coral species. Nonetheless, Proteobacteria was the most abundant phylum in both coral species and was reduced during the southwest (SW) monsoon, while Cyanobacteria and Crenarchaeota increased. The presumptive beneficial endosymbiont Endozoicomonas was only associated with corals at the reef site located the farthest from the Singapore mainland. The coral microbiomes reflected seasonal changes, while the seawater displayed distinct temporal microbial compositions and site-specific differentiation within all sampling dates. The persistence of coral reefs within the port of Singapore highlights the adaptive ability of corals to respond to stressful environments, and this study provides further evidence that a flexible microbiome could be an important part of the strategy employed by corals to remain resilient.

Devlin, C, Chadwick, S, Moret, S, Baechler, S, Raymond, J & Morelato, M 2023, 'The potential of using the forensic profiles of Australian fraudulent identity documents to assist intelligence-led policing', Australian Journal of Forensic Sciences, vol. 55, no. 6, pp. 720-730.
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Dhungana, A, Becchi, S, Leake, J, Morris, G, Avgan, N, Balleine, BW, Vissel, B & Bradfield, LA 2023, 'Goal-Directed Action Is Initially Impaired in a hAPP-J20 Mouse Model of Alzheimer’s Disease', eneuro, vol. 10, no. 2, pp. ENEURO.0363-22.2023.
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AbstractCognitive-behavioral testing in preclinical models of Alzheimer’s disease has failed to capture deficits in goal-directed action control. Here, we provide the first comprehensive investigation of goal-directed action in a transgenic mouse model of Alzheimer’s disease. Specifically, we tested outcome devaluation performance in male and female human amyloid precursor protein (hAPP)-J20 mice. Mice were first trained to press left and right levers for pellet and sucrose outcomes, respectively (counterbalanced), over 4 d. On test, mice were prefed one of the outcomes to satiety and given a choice between levers. Devaluation performance was intact for 36-week-old wild-types of both sexes, who responded more on the valued relative to the devalued lever (Valued > Devalued). By contrast, devaluation was impaired (Valued = Devalued) for J20 mice of both sexes, and for 52-week-old male mice regardless of genotype. After additional lever press training (i.e., 8-d lever pressing in total), devaluation was intact for all mice, demonstrating that the initial deficits were not a result of a nonspecific impairment in reward processing, depression, or locomotor activity in J20 or aging mice. Follow-up analyses revealed that microglial expression in the dorsal CA1 region of the hippocampus was associated with poorer outcome devaluation performance on initial, but not later tests. Together, these data demonstrate that goal-directed action is initially impaired in J20 mice of both sexes and in aging male mice regardless of genotype, and that this impairment is related to neuroinflammation in the dorsal CA1 hippocampal region.

Dickson, K-A, Field, N, Blackman, T, Ma, Y, Xie, T, Kurangil, E, Idrees, S, Rathnayake, SNH, Mahbub, RM, Faiz, A & Marsh, DJ 2023, 'CRISPR single base-editing: in silico predictions to variant clonal cell lines', Human Molecular Genetics, vol. 32, no. 17, pp. 2704-2716.
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Abstract Engineering single base edits using CRISPR technology including specific deaminases and single-guide RNA (sgRNA) is a rapidly evolving field. Different types of base edits can be constructed, with cytidine base editors (CBEs) facilitating transition of C-to-T variants, adenine base editors (ABEs) enabling transition of A-to-G variants, C-to-G transversion base editors (CGBEs) and recently adenine transversion editors (AYBE) that create A-to-C and A-to-T variants. The base-editing machine learning algorithm BE-Hive predicts which sgRNA and base editor combinations have the strongest likelihood of achieving desired base edits. We have used BE-Hive and TP53 mutation data from The Cancer Genome Atlas (TCGA) ovarian cancer cohort to predict which mutations can be engineered, or reverted to wild-type (WT) sequence, using CBEs, ABEs or CGBEs. We have developed and automated a ranking system to assist in selecting optimally designed sgRNA that considers the presence of a suitable protospacer adjacent motif (PAM), the frequency of predicted bystander edits, editing efficiency and target base change. We have generated single constructs containing ABE or CBE editing machinery, an sgRNA cloning backbone and an enhanced green fluorescent protein tag (EGFP), removing the need for co-transfection of multiple plasmids. We have tested our ranking system and new plasmid constructs to engineer the p53 mutants Y220C, R282W and R248Q into WT p53 cells and shown that these mutants cannot activate four p53 target genes, mimicking the behaviour of endogenous p53 mutations. This field will continue to rapidly progress, requiring new strategies such as we propose to ensure desired base-editing outcomes.

Dilernia, NJ, Camp, EF, Bartels, N & Suggett, DJ 2023, 'Contrasting the thermal performance of cultured coral endosymbiont photo-physiology', Journal of Experimental Marine Biology and Ecology, vol. 561, pp. 151865-151865.
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Ding, L, Oh, S, Shrestha, J, Lam, A, Wang, Y, Radfar, P & Warkiani, ME 2023, 'Scaling up stem cell production: harnessing the potential of microfluidic devices', Biotechnology Advances, vol. 69, pp. 108271-108271.
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Ding, Y, Zhang, S, Li, J, Sun, Y, Yin, B, Li, H, Ma, Y, Wang, Z, Ge, H, Su, D & Ma, T 2023, 'Enhanced Elastic Migration of Magnesium Cations in alpha‐Manganese Dioxide Tunnels Locally Tuned by Aluminium Substitution', Advanced Functional Materials, vol. 33, no. 2, pp. 2210519-2210519.
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AbstractThe harsh conditions of large hydrated ion radius of Mg2+ cations and the strong electrostatic interaction with the host material put forward higher requirements for high‐performance aqueous magnesium ion (Mg2+) energy storage devices. Herein, substituted aluminium ions (Al3+) doped α‐MnO2 materials are prepared. The introduction of Al3+ cations adjust the local chemical environment inside the tunnel structure of α‐MnO2 and precisely regulates the diffusion behavior of inserted Mg2+ cations. The shortened oxygens’ distance and abundant oxygen defects result in a substantially enhanced elastic migration pattern of Mg2+ cations driven by strengthened electrostatic attraction, which brings the lower diffusion energy barrier, improved reaction kinetics, and adaptive volume expansion as evidenced by Climbing Image‐Nudged Elastic Band density function theory calculations coupled with experimental confirmation in X‐ray photoelectron spectroscopy, electron paramagnetic resonance, and galvanostatic intermittent titration technique. As a result, this rationally designed cathode exhibits a high reversible capacity of 197.02 mAh g‐1 at 0.1 A g‐1 and stable cycle performance of 2500 cycles with 82% retention. These parameters are among the best of Mg‐ion capacitors reported to date. This study offers a detailed insight into the local tunnel structure tunning effect and opens up a new path of modification for tunnel‐type structural materials.

Doane, MP, Ostrowski, M, Brown, M, Bramucci, A, Bodrossy, L, van de Kamp, J, Bissett, A, Steinberg, P, Doblin, MA & Seymour, J 2023, 'Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions', Environmental Microbiology, vol. 25, no. 6, pp. 1084-1098.
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AbstractBacterioplankton communities govern marine productivity and biogeochemical cycling, yet drivers of bacterioplankton assembly remain unclear. Here, we contrast the relative contribution of deterministic processes (environmental factors and biotic interactions) in driving temporal dynamics of bacterioplankton diversity at three different oceanographic time series locations, spanning 15° of latitude, which are each characterized by different environmental conditions and varying degrees of seasonality. Monthly surface samples (5.5 years) were analysed using 16S rRNA amplicon sequencing. The high‐ and mid‐latitude sites of Maria Island and Port Hacking were characterized by high and intermediate levels of environmental heterogeneity, respectively, with both alpha diversity (72%; 24% of total variation) and beta diversity (32%; 30%) patterns within bacterioplankton assemblages explained by day length, ammonium, and mixed layer depth. In contrast, North Stradbroke Island, a sub‐tropical location where environmental conditions are less variable, interspecific interactions were of increased importance in structuring bacterioplankton diversity (alpha: 33%; beta: 26%) with environment only contributing 11% and 13% to predicting diversity, respectively. Our results demonstrate that bacterioplankton diversity is the result of both deterministic environmental and biotic processes and that the importance of these different deterministic processes varies, potential in response to environmental heterogeneity.

Dong, H, Qi, S, Wang, L, Chen, X, Xiao, Y, Wang, Y, Sun, B, Wang, G & Chen, S 2023, 'Conductive Polymer Coated Layered Double Hydroxide as a Novel Sulfur Reservoir for Flexible Lithium‐Sulfur Batteries', Small, vol. 19, no. 30.
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AbstractLithium‐sulfur battery (LSB) is widely regarded as the most promising next‐generation energy storage system owing to its high theoretical capacity and low cost. However, the practical application of LSBs is mainly hampered by the low electronic conductivity of the sulfur cathode and the notorious “shuttle effect”, which lead to high voltage polarization, severe over‐charge behavior, and rapid capacity decay. To address these issues, a novel sulfur reservoir is synthesized by coating polypyrrole (PPy) thin film on hollow layered double hydroxide (LDH) (PPy@LDH). After compositing with sulfur, such PPy@LDH‐S cathode shows a multi‐functional effect to reserve lithium polysulfides (LiPSs). In addition, the unique architecture provides sufficient inner space to encapsulate the volume expansion and enhances the reaction kinetics of sulfur‐based redox chemistry. Theoretical calculations have illustrated that the PPy@LDH has shown stronger chemical adsorption capability for LiPSs than those of porous carbon and LDH, preventing the shuttling of LiPSs and enhancing the nucleation affinity of liquid‐solid conversion. As a result, the PPy@LDH‐S electrode delivers a stable cycling performance and a superior rate capability. Flexible battery has demonstrated this PPy@LDH‐S electrode can work properly with treatments of bending, folding, and even twisting, paving the way for wearable devices and flexible electronics.

Donovan, C, Barnes, JL & Kim, RY 2023, 'Back to the Eosinophil: Resolvin Spatiotemporal Regulation', American Journal of Respiratory Cell and Molecular Biology, vol. 69, no. 6, pp. 608-609.
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DOOLEY, AH & JIN, JIE 2023, 'A non-singular version of the Oseledeč ergodic theorem', Ergodic Theory and Dynamical Systems, vol. 43, no. 3, pp. 873-886.
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AbstractKingman’s subadditive ergodic theorem is traditionally proved in the setting of a measure-preserving invertible transformation T of a measure space $(X, \mu )$. We use a theorem of Silva and Thieullen to extend the theorem to the setting of a not necessarily invertible transformation, which is non-singular under the assumption that $\mu $ and $\mu \circ T$ have the same null sets. Using this, we are able to produce versions of the Furstenberg–Kesten theorem and the Oseledeč ergodic theorem for products of random matrices without the assumption that the transformation is either invertible or measure-preserving.

Douglas, ANJ, Irga, PJ & Torpy, FR 2023, 'Investigating Vegetation Types Based on the Spatial Variation in Air Pollutant Concentrations Associated with Different Forms of Urban Forestry', Environments, vol. 10, no. 2, pp. 32-32.
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Globally, rapid urbanisation is one of the major drivers for land-use changes, many of which have a marked impact on urban air quality. Urban forestry has been increasingly proposed as a means of reducing airborne pollutants; however, limited studies have comparatively assessed land-use types, including urban forestry, for their relationship with air pollution on a city scale. We, thus, investigated the spatial relationships between three air pollutant concentrations, NO2, SO2, and PM10, and different land uses and land covers across a major city, by constructing a yearly average model combining these variables. Additionally, relationships between different vegetation types and air pollutant concentrations were investigated to determine whether different types of vegetation are associated with different air pollutants. Parklands, water bodies, and more specifically, broadleaf evergreen forest and mangrove vegetation were associated with lower pollutant concentrations. These findings support urban forestry’s capabilities to mitigate air pollution across a city-wide scale.

Dower, A, Mulcahy, M, Maharaj, M, Chen, H, Lim, CED, Li, Y & Sheridan, M 2023, 'Surgical Decompression for Malignant Cerebral Edema After Ischemic Stroke: Cochrane Review', Stroke, vol. 54, no. 12, pp. e500-e502.
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Dowling, NA, Wilson, JR, Cope, JM, Dougherty, DT, Lomonico, S, Revenga, C, Snouffer, BJ, Salinas, NG, Torres‐Cañete, F, Chick, RC, Fowler, AM & Parma, AM 2023, 'The FishPath approach for fisheries management in a data‐ and capacity‐limited world', Fish and Fisheries, vol. 24, no. 2, pp. 212-230.
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AbstractSuccessful fisheries management systems tend to be underpinned by harvest strategies, specifying formally agreed data collection systems, assessment approaches and management measures used to regulate fishing pressure. While harvest strategies can be effective even in data‐ and capacity‐limited (DCL) situations, their development remains challenging in such contexts. We present a process and decision‐support tool, FishPath, to guide the identification of suitable harvest strategy component options given often debilitating conditions: (i) resource limitations and lack of technical management capacity; (ii) ‘uniqueness’ of DCL fisheries; (iii) the concept of harvest strategies is unfamiliar to managers and scientists, and the universe of options is hard to navigate; and (iv) the lack of an effective participatory process to identify solutions tailored to local contexts. These conditions can lead to either management paralysis or generic solutions that may be poor fits to specific conditions. The FishPath Tool uses a diagnostic questionnaire that elicits the key characteristics and specific circumstances of a fishery. It compares these with the requirements of alternative options from an inventory of possible harvest strategy components, identifies where these requirements are met and provides customised, transparent guidance on the appropriateness of component options of a harvest strategy, specific to the fishery of interest and its governance context. The FishPath Process is a facilitated multi‐stakeholder, participatory engagement process aimed to set fisheries on the path to develop a harvest strategy. The FishPath Process and Tool combine to ensure a bottom‐up, documented, transparent, replicable and efficient process.

Drew-Smythe, JJ, Davila, YC, McLean, CM, Hingee, MC, Murray, ML, Webb, JK, Krix, DW & Murray, BR 2023, 'Community perceptions of ecosystem services and disservices linked to urban tree plantings', Urban Forestry & Urban Greening, vol. 82, pp. 127870-127870.
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Duong, K, Maleknia, S, Clases, D, Minett, A, Padula, MP, Doble, PA & Gonzalez de Vega, R 2023, 'Immunoaffinity extraction followed by enzymatic digestion for the isolation and identification of proteins employing automated μSPE reactors and mass spectrometry', Analytical and Bioanalytical Chemistry, vol. 415, no. 18, pp. 4173-4184.
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AbstractThis work describes a novel automated and rapid method for bottom-up proteomics combining protein isolation with a micro-immobilised enzyme reactor (IMER). Crosslinking chemistry based on 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide (EDC/NHS) coupling was exploited to immobilise trypsin and antibodies onto customisable silica particles coated with carboxymethylated dextran (CMD). This novel silica–CMD solid-phase extraction material was characterised using Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), conductometric titrations and enzymatic colorimetric assays. Micro-solid-phase extraction (μSPE) cartridges equipped with the modified CMD material were employed and integrated into an automated and repeatable workflow using a sample preparation workstation to achieve rapid and repeatable protein isolation and pre-concentration, followed by tryptic digestion producing peptide fragments that were identified by liquid chromatography mass spectrometry (LC-MS). Graphical abstract

Dupuy, A, Aponte-Santamaría, C, Yeheskel, A, Hortle, E, Oehlers, SH, Gräter, F, Hogg, PJ, Passam, FH & Chiu, J 2023, 'Mechano-Redox Control of Mac-1 De-Adhesion by PDI Promotes Directional Movement Under Flow', Circulation Research, vol. 132, no. 9.
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Background: Neutrophil migration is critical to the initiation and resolution of inflammation. Macrophage-1 antigen (Mac-1; CD11b/CD18, αMβ2) is a leukocyte integrin essential for firm adhesion to endothelial ICAM-1 (intercellular adhesion molecule 1) and migration of neutrophils in the shear forces of the circulation. PDI (protein disulfide isomerase) has been reported to influence neutrophil adhesion and migration. We aimed to elucidate the molecular mechanism of PDI control of Mac-1 affinity for ICAM-1 during neutrophil migration under fluid shear. Methods: Neutrophils isolated from whole blood were perfused over microfluidic chips coated with ICAM-1. Colocalization of Mac-1 and PDI on neutrophils was visualized by fluorescently labeled antibodies and confocal microscopy. The redox state of Mac-1 disulfide bonds was mapped by differential cysteine alkylation and mass spectrometry. Wild-type or disulfide mutant Mac-1 was expressed recombinantly in Baby Hamster Kidney cells to measure ligand affinity. Mac-1 conformations were measured by conformation-specific antibodies and molecular dynamics simulations. Neutrophils crawling on immobilized ICAM-1 were measured in presence of oxidized or reduced PDI, and the effect of PDI inhibition using isoquercetin on neutrophil crawling on inflamed endothelial cells was examined. Migration indices in the X- and Y-direction were determined and the crawling speed was calculated. Results: PDI colocalized with high-affinity Mac-1 at the trailing edge of stimulated neutrophils when crawling on ICAM-1 under fluid shear. PDI cleaved 2 allosteric disulfide bonds, C169-C176 and C224-C264, in the βI domain of the β2 subunit, and cleavage of the...

Egwunye, J, Cardoso, BR, Braat, S, Ha, T, Hanieh, S, Hare, D, Duan, AX, Doronila, A, Tran, T, Tuan, T, Fisher, J & Biggs, B-A 2023, 'The role of fingernail selenium in the association between arsenic, lead and mercury and child development in rural Vietnam: a cross-sectional analysis', British Journal of Nutrition, vol. 129, no. 9, pp. 1589-1597.
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AbstractAs, Pb and Hg are common environmental contaminants in low- and middle-income countries. We investigated the association between child toxicant exposure and growth and development and determined if this association was mitigated by Se concentration. Toxicant concentrations in fingernail samples, anthropometry and Bayley’s Scales of Infant Development, 3rd edition domains were assessed in 36-month-old children whose mothers had been part of a randomised controlled trial in rural Vietnam. Multivariable regression analyses were performed to estimate the effect of toxicant exposure on clinical outcomes with adjustments for potential confounders and interaction with fingernail Se concentration. We analysed 658 children who had data for at least one physical or developmental outcome, and at least one toxicant measurement, and each of the covariates. Fingernail As concentration was negatively associated with language (estimate per 10 % increase in As: −0·19, 95 % CI: (–0·32, −0·05)). Pb was negatively associated with cognition (estimate per 10 % increase in Pb: −0·08 (–0·15, −0·02)), language (estimate per 10 % increase in Pb: −0·18 (–0·28, −0·10)) and motor skills (estimate per 10 % increase in Pb: −0·12 (–0·24, 0·00)). Hg was negatively associated with cognition (estimate per 10 % increase in Hg: −0·48, (–0·72, −0·23)) and language (estimate per 10 % increase in Hg −0·51, (–0·88, −0·13)) when Se concentration was set at zero in the model. As Se concentration increased, the negative associations between Hg and both cognition and language scores were attenuated. There was no association between toxicant concentration and growth. As, Pb and Hg concentrations in fingernails of 3-year-old children were associated with lower child development scores. The negative association between Hg and neurological development was reduced in magnitude with increasing Se concentration. Se status should be considered when assessing heavy ...

Elankumuran, P, Browning, GF, Marenda, MS, Kidsley, A, Osman, M, Haenni, M, Johnson, JR, Trott, DJ, Reid, CJ & Djordjevic, SP 2023, 'Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans', Microbial Genomics, vol. 9, no. 2, p. mgen000930.
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ST372 are widely reported as the major Escherichia coli sequence type in dogs globally. They are also a sporadic cause of extraintestinal infections in humans. Despite this, it is unknown whether ST372 strains from dogs and humans represent shared or distinct populations. Furthermore, little is known about genomic traits that might explain the prominence of ST372 in dogs or presence in humans. To address this, we applied a variety of bioinformatics analyses to a global collection of 407 ST372 E. coli whole-genome sequences to characterize their epidemiological features, population structure and associated accessory genomes. We confirm that dogs are the dominant host of ST372 and that clusters within the population structure exhibit distinctive O:H types. One phylogenetic cluster, ‘cluster M', comprised almost half of the sequences and showed the divergence of two human-restricted clades that carried different O:H types to the remainder of the cluster. We also present evidence supporting transmission between dogs and humans within different clusters of the phylogeny, including M. We show that multiple acquisitions of the pdu propanediol utilization operon have occurred in clusters dominated by isolates of canine source, possibly linked to diet, whereas loss o...

Elder, M, Piggott, A & Townsend, K 2023, 'On k-geodetic graphs and groups', International Journal of Algebra and Computation, vol. 33, no. 06, pp. 1169-1182.
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We call a graph k-geodetic, for some [Formula: see text], if it is connected and between any two vertices there are at most k geodesics. It is shown that any hyperbolic group with a k-geodetic Cayley graph is virtually-free. Furthermore, in such a group the centralizer of any infinite order element is an infinite cyclic group. These results were known previously only in the case that [Formula: see text]. A key tool used to develop the theorem is a new graph theoretic result concerning “ladder-like structures” in a k-geodetic graph.

Ellis, JT & Reichel, MP 2023, 'Twitter trends in #Parasitology determined by text mining and topic modelling', Current Research in Parasitology & Vector-Borne Diseases, vol. 4, pp. 100138-100138.
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This study investigated the emergence and use of Twitter, as of July 2023 being rebranded as X, as the main forum for social media communication in parasitology. A dataset of tweets was constructed using a keyword search of Twitter with the search terms 'malaria', 'Plasmodium', 'Leishmania', 'Trypanosoma', 'Toxoplasma' and 'Schistosoma' for the period from 2011 to 2020. Exploratory data analyses of tweet content were conducted, including language, usernames and hashtags. To identify parasitology topics of discussion, keywords and phrases were extracted using KeyBert and biterm topic modelling. The sentiment of tweets was analysed using VADER. The results show that the number of tweets including the keywords increased from 2011 (for malaria) and 2013 (for the others) to 2020, with the highest number of tweets being recorded in 2020. The maximum number of yearly tweets for Plasmodium, Leishmania, Toxoplasma, Trypanosoma and Schistosoma was recorded in 2020 (2804, 2161, 1570, 680 and 360 tweets, respectively). English was the most commonly used language for tweeting, although the percentage varied across the searches. In tweets mentioning Leishmania, only ∼37% were in English, with Spanish being more common. Across all the searches, Portuguese was another common language found. Popular tweets on Toxoplasma contained keywords relating to mental health including depression, anxiety and schizophrenia. The Trypanosoma tweets referenced drugs (benznidazole, nifurtimox) and vectors (bugs, triatomines, tsetse), while the Schistosoma tweets referenced areas of biology including pathology, eggs and snails. A wide variety of individuals and organisations were shown to be associated with Twitter activity. Many journals in the parasitology arena regularly tweet about publications from their journal, and professional societies promote activity and events that are important to them. These represent examples of trusted sources of information, often by experts in their fi...

Elrahoumi, R, Zhu, L, Wagner, E, Maudez, W, Benvenuti, G, Phillips, MR & Ton-That, C 2023, 'Doping-induced Ti3+ state and oxygen vacancies in TiO2: A single-chip combinatorial investigation', Materials Chemistry and Physics, vol. 308, pp. 128283-128283.
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Eskandrani, A, Paudel, KR, Elwakil, BH, Bakr, BA, Darwish, AA-E, Akl, SH, Shahin, YH, Moneer, EA & Atef, AM 2023, 'The potent synergistic effect of Brassica oleracea against congenital Toxoplasma infection in rat model', Food Bioscience, vol. 55, pp. 103059-103059.
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Congenital toxoplasmosis is among the leading causes of fetus damage and abortion. Pyrimethamine + sulfadiazine is usually the chosen treatment against toxoplasmosis during pregnancy. Severe cutaneous adverse responses, teratogenicity, and changes in bilirubin metabolism are just a few examples of the pyrimethamine + sulfadiazine's toxicity. The present study aimed to assess the potent effect of a Brassica oleracea-based diet to synergistically enhance the effect of pyrimethamine + sulfadiazine in combating congenital toxoplasmosis and reduce the drug adverse effects. Broccoli (Brassica oleracea) was included in a standard pellet diet for the T. gondii infected pregnant rats. At the end of the experiment interleukins (IL-6, IL- 10), TNF-α, NF-κB and IFN-γ levels, biochemical analyses, parasite count and histopathological studies were assessed. A noticeable decrement was observed in the combination treated rat group (pyrimethamine + sulfadiazine and broccoli-based diet feed). Moreover, the biochemical analysis further validated the potent combined therapy effectiveness. The parasitological study revealed that the mean tachyzoites count was the lowest among pregnant rats and the offspring group after receiving the formulated combined treatment. Moreover, the histopathological studies revealed that the combined treatment had a significant synergistic effect on the tissues of spleen and liver. While the cerebral cortex of fetuses maternally fed on the broccoli-based diet showed mild symptoms of damage with normal neurons. Taken together, the broccoli-based diet enhanced the immunological, biochemical, and histological responses against toxoplasmosis and also decreased the vertical transmission of congenital toxoplasmosis.

Eslami, A, Nassif, NT & Lal, S 2023, 'Evaluating High and Low Heart Rate Variability Response and Neurocognitive Performance in Workers: An Exploratory Study', Behavioral Sciences, vol. 13, no. 9, pp. 742-742.
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Heart rate variability (HRV) has the potential to be a predicting factor of cognitive performance. The present research aimed to explore the differences in neurocognitive performance of workers with high HRV and low HRV. A total of 48 white-collar workers and 53 blue-collar workers were assessed. An electrocardiogram was used to obtain HRV data, whereby a 10 min baseline and an active (neuropsychological task) recording were taken. Median splits were performed on data to obtain high- and low-HRV groups. The Cambridge Neuropsychological Test Automated Battery, specifically, the spatial working memory, attention-switching task, rapid visual processing, and spatial span were used. Higher HRV (RMSSD and HF) was linked to better neurocognitive performance measures. Interestingly, the blue- and white-collar groups exhibited different correlations and, in some cases, showed an inverse relationship with the same variables. The differences observed in the present study demonstrate the importance of assessing task-dependent HRV parameters.

Fairley, LH, Das, S, Dharwal, V, Amorim, N, Hegarty, KJ, Wadhwa, R, Mounika, G & Hansbro, PM 2023, 'Mitochondria-Targeted Antioxidants as a Therapeutic Strategy for Chronic Obstructive Pulmonary Disease', Antioxidants, vol. 12, no. 4, pp. 973-973.
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Oxidative stress is a major hallmark of COPD, contributing to inflammatory signaling, corticosteroid resistance, DNA damage, and accelerated lung aging and cellular senescence. Evidence suggests that oxidative damage is not solely due to exogenous exposure to inhaled irritants, but also endogenous sources of oxidants in the form of reactive oxygen species (ROS). Mitochondria, the major producers of ROS, exhibit impaired structure and function in COPD, resulting in reduced oxidative capacity and excessive ROS production. Antioxidants have been shown to protect against ROS-induced oxidative damage in COPD, by reducing ROS levels, reducing inflammation, and protecting against the development of emphysema. However, currently available antioxidants are not routinely used in the management of COPD, suggesting the need for more effective antioxidant agents. In recent years, a number of mitochondria-targeted antioxidant (MTA) compounds have been developed that are capable of crossing the mitochondria lipid bilayer, offering a more targeted approach to reducing ROS at its source. In particular, MTAs have been shown to illicit greater protective effects compared to non-targeted, cellular antioxidants by further reducing apoptosis and offering greater protection against mtDNA damage, suggesting they are promising therapeutic agents for the treatment of COPD. Here, we review evidence for the therapeutic potential of MTAs as a treatment for chronic lung disease and discuss current challenges and future directions.

Fairley, LH, Lai, KO, Wong, JH, Chong, WJ, Vincent, AS, D’Agostino, G, Wu, X, Naik, RR, Jayaraman, A, Langley, SR, Ruedl, C & Barron, AM 2023, 'Mitochondrial control of microglial phagocytosis by the translocator protein and hexokinase 2 in Alzheimer’s disease', Proceedings of the National Academy of Sciences, vol. 120, no. 8.
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Microglial phagocytosis is an energetically demanding process that plays a critical role in the removal of toxic protein aggregates in Alzheimer’s disease (AD). Recent evidence indicates that a switch in energy production from mitochondrial respiration to glycolysis disrupts this important protective microglial function and may provide therapeutic targets for AD. Here, we demonstrate that the translocator protein (TSPO) and a member of its mitochondrial complex, hexokinase-2 (HK), play critical roles in microglial respiratory-glycolytic metabolism and phagocytosis. Pharmacological and genetic loss-of-function experiments showed that TSPO is critical for microglial respiratory metabolism and energy supply for phagocytosis, and its expression is enriched in phagocytic microglia of AD mice. Meanwhile, HK controlled glycolytic metabolism and phagocytosis via mitochondrial binding or displacement. In cultured microglia, TSPO deletion impaired mitochondrial respiration and increased mitochondrial recruitment of HK, inducing a switch to glycolysis and reducing phagocytosis. To determine the functional significance of mitochondrial HK recruitment, we developed an optogenetic tool for reversible control of HK localization. Displacement of mitochondrial HK inhibited glycolysis and improved phagocytosis in TSPO-knockout microglia. Mitochondrial HK recruitment also coordinated the inflammatory switch to glycolysis that occurs in response to lipopolysaccharide in normal microglia. Interestingly, cytosolic HK increased phagocytosis independent of its metabolic activity, indicating an immune signaling function. Alzheimer’s beta amyloid drastically stimulated mitochondrial HK recruitment in cultured microglia, which may contribute to microglial dysfunction in AD. Thus, targeting mitochondrial HK may offer an immunotherapeutic approach to promote phagocytic microglial function in AD.

Faiz, A, Mahbub, RM, Boedijono, FS, Tomassen, MI, Kooistra, W, Timens, W, Nawijn, M, Hansbro, PM, Johansen, MD, Pouwels, SD, Heijink, IH, Massip, F, de Biase, MS, Schwarz, RF, Adcock, IM, Chung, KF, van der Does, A, Hiemstra, PS, Goulaouic, H, Xing, H, Abdulai, R, de Rinaldis, E, Cunoosamy, D, Harel, S, Lederer, D, Nivens, MC, Wark, PA, Kerstjens, HAM, Hylkema, MN, Brandsma, C-A & van den Berge, M 2023, 'IL-33 Expression Is Lower in Current Smokers at both Transcriptomic and Protein Levels', American Journal of Respiratory and Critical Care Medicine, vol. 208, no. 10, pp. 1075-1087.
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INTRODUCTION: IL-33 is a pro-inflammatory cytokine thought to play a role in the pathogenesis of asthma and COPD. A recent clinical trial using the anti-IL33 antibody showed a reduction in exacerbation and improved lung function in ex-smokers but not current smokers with COPD. In this study, we aimed to understand the effects of smoking status on IL-33. METHODS: We investigated the association of smoking status with the level of gene expression of IL33 in the airways in eight independent transcriptomic studies of lung airways. Additionally, we performed western blot and immunohistochemistry for IL-33 in lung tissue to assess protein levels. RESULTS: Across the bulk RNA-sequencing datasets, IL-33 gene expression and its signaling pathway were significantly lower in current- compared to ex- or never-smokers and increased upon smoking cessation (p<0.05). Single-cell sequencing showed that IL-33 is predominantly expressed in resting basal epithelial cells and decreases during the differentiation process triggered by smoke exposure. We also found a higher transitioning of this cellular sub-population into a more differentiated cell type during chronic smoking, potentially driving the reduction of IL-33. Protein analysis demonstrated lower IL-33 levels in lung tissue from COPD current- compared to ex-smokers and a lower proportion of IL-33 positive basal cells in current versus ex-smoking controls. CONCLUSION: We provide strong evidence that cigarette smoke leads to an overall reduction in IL33 expression in both transcriptomic and protein level and this may be due to the decrease in resting basal cells. Together, these findings may explain the clinical observation that a recent antibody-based anti-IL-33 treatment is more effective in ex- than current smokers with COPD. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Faiz, A, Pavlidis, S, Kuo, C-H, Rowe, A, Hiemstra, PS, Timens, W, Berg, M, Wisman, M, Guo, Y-K, Djukanović, R, Sterk, P, Meyer, KB, Nawijn, MC, Adcock, I, Chung, KF & van den Berge, M 2023, 'Th2 high and mast cell gene signatures are associated with corticosteroid sensitivity in COPD', Thorax, vol. 78, no. 4, pp. 335-343.
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RationaleSevere asthma and chronic obstructive pulmonary disease (COPD) share common pathophysiological traits such as relative corticosteroid insensitivity. We recently published three transcriptome-associated clusters (TACs) using hierarchical analysis of the sputum transcriptome in asthmatics from the Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes (U-BIOPRED) cohort comprising one Th2-high inflammatory signature (TAC1) and two Th2-low signatures (TAC2 and TAC3).ObjectiveWe examined whether gene expression signatures obtained in asthma can be used to identify the subgroup of patients with COPD with steroid sensitivity.MethodsUsing gene set variation analysis, we examined the distribution and enrichment scores (ES) of the 3 TACs in the transcriptome of bronchial biopsies from 46 patients who participated in the Groningen Leiden Universities Corticosteroids in Obstructive Lung Disease COPD study that received 30 months of treatment with inhaled corticosteroids (ICS) with and without an added long-acting β-agonist (LABA). The identified signatures were then associated with longitudinal clinical variables after treatment. Differential gene expression and cellular convolution were used to define key regulated genes and cell types.Measurements and main resultsBronchial biopsies in patients with COPD at baseline showed a wide range of expression of the 3 TAC signatures. After ICS±LABA treatment, the ES of TAC1 was significantly reduced at 30 months, but those of TAC2 and TAC3 were unaffected. A corticosteroid-sensitive TAC1 signature was developed from the TAC1 ICS-responsive genes. This signature consisted of mast cell-specific genes identified by single-cell RNA-sequencing and positively correlated with b...

Fang, G, Chen, Y, Lu, H & Jin, D 2023, 'Advances in Spheroids and Organoids on a Chip', Advanced Functional Materials, vol. 33, no. 19, pp. 2215043-2215043.
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AbstractMulticellular spheroids and organoids are promising in vitro 3D models in personalized medicine and drug screening. They replicate the structural and functional characteristics of human organs in vivo. Microfluidic technology and micro‐nano fabrication can fulfill the high requirement of the engineering approach in the growing research interest in spheroids and organoids. In this review, spheroids and organoids are comparatively introduced. Then it is illustrated how spheroids‐ and organoids‐on‐a‐chip technology facilitates their establishment, expansion, and application through spatial‐temporal control, mechanical cues modeling, high‐throughput analysis, co‐culture, multi‐tissue interactions, biosensing, and bioimaging integration. The potential opportunities and challenges in developing spheroids‐ and organoids‐on‐a‐chip technology are finally outlooked.

Farahmandjou, M, Lai, W, Safaei, J, Wang, S, Huang, Z, Marlton, F, Ruan, J, Sun, B, Gao, H, Ostrikov, KK, Notten, PHL & Wang, G 2023, 'Boosting the Electrochemical Performance of Lithium‐Rich Cathodes by Oxygen Vacancy Engineering', Batteries & Supercaps, vol. 6, no. 7.
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AbstractThe challenges of voltage decay and irreversible oxygen release for lithium‐rich layered oxide cathode materials have hindered their commercial application despite their high energy density and low cost. Herein, a facile post‐annealing strategy is developed to pre‐introduce oxygen vacancies (OVs) into Li1.2Mn0.457Ni0.229Co0.114O2 cathode materials. The induced OVs modify the local Mn coordination environments, enhance structural stability, and suppress oxygen release. The modified cathode exhibits a discharge capacity of 224.1 mAh g−1 at 0.1 C after 100 cycles with 97.7 % capacity retention. Even at 2 C, excellent capacity retention of 93.3 % after 300 cycles can be achieved. In situ and ex situ X‐ray diffraction are used to elucidate the reaction mechanisms and crystal structure during cycling tests. Ex situ X‐ray photoelectron spectroscopy confirmed the suppressed oxygen release, enhanced oxygen vacancies and reduced cathode‐electrolyte interfacial layer after cycling for the post‐annealed cathode. Our results show that the presence of oxygen vacancies through thermal expansion diminishes the phase transitions in cathode materials during the heating process. These findings contribute to developing next‐generation Li‐ion batteries (LIBs) by oxygen vacancy engineering for new cathode materials with improved electrochemical performances.

Farahmandjou, M, Lai, W, Safaei, J, Wang, S, Huang, Z, Marlton, F, Ruan, J, Sun, B, Gao, H, Ostrikov, KK, Notten, PHL & Wang, G 2023, 'Cover Feature: Boosting the Electrochemical Performance of Lithium‐Rich Cathodes by Oxygen Vacancy Engineering (Batteries & Supercaps 7/2023)', Batteries & Supercaps, vol. 6, no. 7.
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Fares, M, Wu, X, McNaughton, DA, Gilchrist, AM, Lewis, W, Keller, PA, Arias-Betancur, A, Fontova, P, Pérez-Tomás, R & Gale, PA 2023, 'A potent fluorescent transmembrane HCl transporter perturbs cellular pH and promotes cancer cell death', Organic & Biomolecular Chemistry, vol. 21, no. 12, pp. 2509-2515.
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A series of fluorescent coumarin-based bis-ureas have been synthesised. These compounds show strong HCl cotransport properties in model vesicle systems. Cellular localisation studies show that cytotoxic compound 4 localises in lysosomes and perturbs cellular pH.

Favaloro, J, Bryant, CE, Abadir, E, Gardiner, S, Yang, S, King, T, Nassif, N, Sedger, LM, Boyle, R, Joshua, DE & Ho, PJ 2023, 'Single cell analysis of the CD8⁺ T-cell compartment in multiple myeloma reveals disease specific changes are chiefly restricted to a CD69^- subset suggesting potent cytotoxic effectors exist within the tumor bed.', Haematologica.
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Multiple Myeloma (MM) is an incurable disease of the bone marrow (BM) characterized by the uncontrolled proliferation of neoplastic plasma cells. While CD8+ T-cells have an established role in disease control, few studies have focused on these cells within the MM tumor microenvironment (TME). We analyzed CD8+ T-cells in the BM and peripheral blood (PB) of untreated patients with MM and non-myeloma controls using flow cytometry, mass cytometry and single-cell RNA sequencing, using several novel bioinformatics workflows. Inter-tissue differences were most evident in the differential expression of granzymes B and K, which were strongly associated with two distinct subsets of CD8+ T-cells delineated by the expression of CD69, accounting for roughly 50% of BM-CD8+ T-cells of all assessed cohorts. While few differences were observable between health and disease in the BM-restricted CD8CD69+ T-cell subset, the CD8+CD69- T-cell subset in the BM of untreated MM patients demonstrated increased representation of highly differentiated effector cells and evident compositional parallels between the PB, absent in age-matched controls, where a marked reduction of effector cells was observed. We demonstrate the transcriptional signature of BM-CD8+ T-cells from patients with MM more closely resembles TCR-activated CD8+ T-cells from age-matched controls than their resting counterparts.

Feng, Z, Zhu, R, Chen, F, Zhu, Y, Zhou, Y, Guan, P, Kuo, Y-C, Fan, J, Wan, T, Li, M, Han, Z, Su, D & Chu, D 2023, 'Recent advances in water-induced electricity generation based on 2D materials: A review', Journal of Materials Research, vol. 38, no. 7, pp. 1757-1779.
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Fergusson, K & Platen, E 2023, 'Less-expensive long-term annuities linked to mortality, cash and equity', Annals of Actuarial Science, vol. 17, no. 1, pp. 170-207.
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AbstractThis paper proposes a shift in the valuation and production of long-term annuities, away from the classical risk-neutral methodology towards a methodology using the real-world probability measure. The proposed production method is applied to three examples of annuity products, one having annual payments linked to a mortality index and the savings account and the others having annual payments linked to a mortality index and an equity index with a guarantee that is linked to the same mortality index and the savings account. Out-of-sample hedge simulations demonstrate the effectiveness of the proposed less-expensive production method. In contrast to classical risk-neutral production, which revolves around the savings account as reference unit, the long-term best-performing portfolio, the numéraire portfolio of the equity market, is employed as the fundamental reference unit in the production of the annuity. The numéraire portfolio is the strictly positive, tradable portfolio that when used as denominator or benchmark makes all benchmarked non-negative portfolios supermartingales. Under real-world valuation, the initial benchmarked value of a benchmarked contingent claim equals its real-world conditional expectation. The proposed real-world valuation and production can lead to significantly lower values of long-term annuities and their less-expensive production than suggested by the risk-neutral approach.

Fiedler, S, Ton-That, C & Phillips, MR 2023, 'Defect-free ZnO nanorods with high angular distribution for enhanced excitonic emission', Journal of Materials Research, vol. 38, no. 8, pp. 2145-2155.
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AbstractLow-temperature hydrothermal growth has emerged as a popular method for the fabrication of ZnO nanorods (NRs), increasing the functionality and utility of ZnO-based devices. In this work, we study the influence of growth time, temperature and seed layer on the dimensions and angular distribution of ZnO NRs. High-quality NRs with a crisscrossed 60° angular distribution have been grown with a 20–60 nm diameter and 600 nm length. We show that, within the ideal range of growth parameters, the growth time and temperature have no controllable influence on NR diameter and length, while the deposition method and size of the pre-growth deposited ZnO seeds affects diameter and NR angular alignment. We demonstrate advantages of using crisscross-aligned NRs over planar ZnO for the enhancement of ZnO excitonic emission by optical coupling with gold nanoparticles. These results can be readily adapted for applications that involve surface coating-mediated enhancement of both light emission and injection. Graphical abstract

Filippini, G, Bugnot, AB, Varkey, DR, Siboni, N, Ferguson, A, Gribben, PE, Erickson, K, Palmer, J & Dafforn, KA 2023, 'Nitrogen-cycling genes in oyster reefs and surrounding sediments: Relationships with environmental factors and respective nitrogen rates', Marine Pollution Bulletin, vol. 197, pp. 115710-115710.
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Firme, GF, Hughes, DJ, Laiolo, L, Roughan, M, Suthers, IM & Doblin, MA 2023, 'Contrasting phytoplankton composition and primary productivity in multiple mesoscale eddies along the East Australian coast', Deep Sea Research Part I: Oceanographic Research Papers, vol. 193, pp. 103952-103952.
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Fisher, NL, Halsey, KH, Suggett, DJ, Pombrol, M, Ralph, PJ, Lutz, A, Sogin, EM, Raina, J-B & Matthews, JL 2023, 'Light-dependent metabolic shifts in the model diatom Thalassiosira pseudonana', Algal Research, vol. 74, pp. 103172-103172.
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Fleming, CL, Golzan, M, Gunawan, C & McGrath, KC 2023, 'Systematic and Bibliometric Analysis of Magnetite Nanoparticles and Their Applications in (Biomedical) Research', Global Challenges, vol. 7, no. 1, pp. 2200009-2200009.
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AbstractRecent reports show air pollutant magnetite nanoparticles (MNPs) in the brains of people with Alzheimer's disease (AD). Considering various field applications of MNPs because of developments in nanotechnology, the aim of this study is to identify major trends and data gaps in research on magnetite to allow for relevant environmental and health risk assessment. Herein, a bibliometric and systematic analysis of the published magnetite literature (n = 31 567) between 1990 to 2020 is completed. Following appraisal, publications (n = 244) are grouped into four time periods with the main research theme identified for each as 1990–1997 “oxides,” 1998–2005 “ferric oxide,” 2006–2013 “pathology,” and 2014–2020 “animal model.” Magnetite formation and catalytic activity dominate the first two time periods, with the last two focusing on the exploitation of nanoparticle engineering. Japan and China have the highest number of citations for articles published. Longitudinal analysis indicates that magnetite research for the past 30 years shifted from environmental and industrial applications, to biomedical and its potential toxic effects. Therefore, whilst this study presents the research profile of different countries, the development in research on MNPs, it also reveals that further studies on the effects of MNPs on human health is much needed.

Fourment, M, Swanepoel, CJ, Galloway, JG, Ji, X, Gangavarapu, K, Suchard, MA & Matsen IV, FA 2023, 'Automatic Differentiation is no Panacea for Phylogenetic Gradient Computation', Genome Biology and Evolution, vol. 15, no. 6.
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Abstract Gradients of probabilistic model likelihoods with respect to their parameters are essential for modern computational statistics and machine learning. These calculations are readily available for arbitrary models via “automatic differentiation” implemented in general-purpose machine-learning libraries such as TensorFlow and PyTorch. Although these libraries are highly optimized, it is not clear if their general-purpose nature will limit their algorithmic complexity or implementation speed for the phylogenetic case compared to phylogenetics-specific code. In this paper, we compare six gradient implementations of the phylogenetic likelihood functions, in isolation and also as part of a variational inference procedure. We find that although automatic differentiation can scale approximately linearly in tree size, it is much slower than the carefully implemented gradient calculation for tree likelihood and ratio transformation operations. We conclude that a mixed approach combining phylogenetic libraries with machine learning libraries will provide the optimal combination of speed and model flexibility moving forward.

Fowler, AM, Dowling, NA, Lyle, JM, Alós, J, Anderson, LE, Cooke, SJ, Danylchuk, AJ, Ferter, K, Folpp, H, Hutt, C, Hyder, K, Lew, DK, Lowry, MB, Lynch, TP, Meadows, N, Mugerza, E, Nedreaas, K, Garrone‐Neto, D, Ochwada‐Doyle, FA, Potts, W, Records, D, Steinback, S, Strehlow, HV, Tracey, SR, Travis, MD, Tsuboi, J, Vølstad, JH & Chick, RC 2023, 'Toward sustainable harvest strategies for marine fisheries that include recreational fishing', Fish and Fisheries, vol. 24, no. 6, pp. 1003-1019.
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AbstractRecreational fishing (RF) is a large yet undervalued component of fisheries globally. While progress has been made in monitoring, assessing, and managing the sector in isolation, integration of RF into the management of multi‐sector fisheries has been limited, particularly relative to the commercial sector. This marginalises recreational fishers and reduces the likelihood of achieving the sector's objectives and, more broadly, achieving fisheries sustainability. We examined the nature and extent of RF inclusion in harvest strategies (HSs) for marine fisheries across 15 regions in 11 nations to define the gap in inclusion that has developed between sectors. We focused on high‐income nations with a high level of RF governance and used a questionnaire to elicit expert knowledge on HSs due to the paucity of published documents. In total, 339 HSs were considered. We found that RF inclusion in HSs was more similar to the small‐scale sector (i.e., artisanal, cultural, or subsistence) than the commercial sector, with explicit operational objectives, data collection, performance indicators, reference points, and management controls lacking in many regions. Where specified, RF objectives focused on sustainability, economic value and catch allocation rather than directly relating to the recreational fishing experience. Conflicts with other sectors included competition with the commercial sector for limited resources, highlighting the importance of equitable resource allocation policies alongside HSs. We propose that RF be explicitly incorporated into HSs to ensure fisheries are ecologically, economically, and socially sustainable, and we recommend that fisheries organisations urgently review HSs for marine fisheries with a recreational component to close the harvest strategy gap among sectors.

Froehlich, CYM, Klanten, OS, Hing, ML, Dowton, M & Wong, MYL 2023, 'Delayed recovery and host specialization may spell disaster for coral‐fish mutualism', Ecology and Evolution, vol. 13, no. 6.
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AbstractMutualisms are prevalent in many ecosystems, yet little is known about how symbioses are affected by ecological pressures. Here, we show delayed recovery for 13 coral‐dwelling goby fishes (genus Gobiodon) compared with their host Acropora corals following four consecutive cyclones and heatwaves. While corals became twice as abundant in 3 years postdisturbances, gobies were only half as abundant relative to predisturbances and half of the goby species disappeared. Although gobies primarily occupied one coral species in greater abundance predisturbances, surviving goby species shifted hosts to newly abundant coral species when their previously occupied hosts became rare postdisturbances. As host specialization is key for goby fitness, shifting hosts may have negative fitness consequences for gobies and corals alike and affect their survival in response to environmental changes. Our study is an early sign that mutualistic partners may not recover similarly from multiple disturbances, and that goby host plasticity, while potentially detrimental, may be the only possibility for early recovery.

Fronzi, M, Ellis, A & Goudeli, E 2023, 'Silicon-Based Anodes for Li Batteries: Thermodynamics, Structural Analysis, and Li Diffusion', The Journal of Physical Chemistry Letters, vol. 14, no. 46, pp. 10388-10395.
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Fu, S, Shi, W, Luo, T, He, Y, Zhou, L, Yang, J, Yang, Z, Liu, J, Liu, X, Guo, Z, Yang, C, Liu, C, Huang, Z-L, Ries, J, Zhang, M, Xi, P, Jin, D & Li, Y 2023, 'Field-dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging', Nature Methods, vol. 20, no. 3, pp. 459-468.
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Gale, A, Scognamiglio, D, Zhigulin, I, Whitefield, B, Kianinia, M, Aharonovich, I & Toth, M 2023, 'Manipulating the Charge State of Spin Defects in Hexagonal Boron Nitride', Nano Letters, vol. 23, no. 13, pp. 6141-6147.
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Gallagher, CI, Frangos, ZJ, Sheipouri, D, Shimmon, S, Duman, M-N, Jayakumar, S, Cioffi, CL, Rawling, T & Vandenberg, RJ 2023, 'Novel Phenylene Lipids That Are Positive Allosteric Modulators of Glycine Receptors and Inhibitors of Glycine Transporter 2', ACS Chemical Neuroscience, vol. 14, no. 15, pp. 2634-2647.
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Gao, X, Yang, N, Feng, J, Liao, J, Hou, S, Ma, X, Su, D, Yu, X, Yang, Z, Safaei, J, Wang, D & Wang, G 2023, 'Defect and interface control on graphitic carbon nitrides/upconversion nanocrystals for enhanced solar hydrogen production', National Science Open, vol. 2, no. 2, pp. 20220037-20220037.
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Geilen, A, Popp, A, Das, D, Junaid, S, Poulton, CG, Chemnitz, M, Marquardt, C, Schmidt, MA & Stiller, B 2023, 'Extreme thermodynamics in nanolitre volumes through stimulated Brillouin–Mandelstam scattering', Nature Physics, vol. 19, no. 12, pp. 1805-1812.
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AbstractExamining the physical properties of materials—particularly of toxic liquids—under a wide range of thermodynamic states is a challenging problem due to the extreme conditions the material has to experience. Such temperature and pressure regimes, which result in a change in the refractive index and sound velocity, can be accessed by optoacoustic interactions such as Brillouin–Mandelstam scattering. Here we demonstrate the Brillouin–Mandelstam measurements of nanolitre volumes of liquids in extreme thermodynamic regimes. This is enabled by a fully sealed liquid-core optical fibre containing carbon disulfide. Within this waveguide, which exhibits tight optoacoustic confinement and a high Brillouin gain, we are able to conduct spatially resolved measurements of the local Brillouin response, giving us access to a resolved image of the temperature and pressure values along the liquid channel. We measure the material properties of the liquid core at very large positive pressures (above 1,000 bar) and substantial negative pressures (below –300 bar), as well as explore the isobaric and isochoric regimes. The extensive thermodynamic control allows the tunability of the Brillouin frequency shift of more than 40% using only minute volumes of liquid.

Gera, T, Chen, L, Eisfeld, A, Reimers, JR, Taffet, EJ & Raccah, DIGB 2023, 'Simulating optical linear absorption for mesoscale molecular aggregates: An adaptive hierarchy of pure states approach', The Journal of Chemical Physics, vol. 158, no. 17.
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In this paper, we present dyadic adaptive HOPS (DadHOPS), a new method for calculating linear absorption spectra for large molecular aggregates. This method combines the adaptive HOPS (adHOPS) framework, which uses locality to improve computational scaling, with the dyadic HOPS method previously developed to calculate linear and nonlinear spectroscopic signals. To construct a local representation of dyadic HOPS, we introduce an initial state decomposition that reconstructs the linear absorption spectra from a sum over locally excited initial conditions. We demonstrate the sum over initial conditions can be efficiently Monte Carlo sampled and that the corresponding calculations achieve size-invariant [i.e., O(1)] scaling for sufficiently large aggregates while trivially incorporating static disorder in the Hamiltonian. We present calculations on the photosystem I core complex to explore the behavior of the initial state decomposition in complex molecular aggregates as well as proof-of-concept DadHOPS calculations on an artificial molecular aggregate inspired by perylene bis-imide to demonstrate the size-invariance of the method.

Geronimo, F 2023, 'Current debates and research in cardiovascular medicine', Medical Journal of Australia, vol. 219, no. 4, pp. 139-139.
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Gertner, DS, Bishop, DP & Padula, MP 2023, 'Optimization of chromatographic buffer conditions for the simultaneous analysis of phosphatidylinositol and phosphatidylinositol phosphate species in canola', Journal of Separation Science, vol. 46, no. 16, p. e2300165.
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The phosphatidylinositols and phosphatidylinositol phosphates are a set of closely related lipids known to influence various cellular functions. Irregular distributions of these molecules have been correlated with the development and progression of multiple diseases, including Alzheimer's, bipolar disorder, and various cancers. As a result, there is continued interest regarding the speciation of these compounds, with specific consideration on how their distribution may differ between healthy and diseased tissue. The comprehensive analysis of these compounds is challenging due to their varied and unique chemical characteristics, and current generalized lipidomics methods have proven unsuitable for phosphatidylinositol analysis and remain incapable of phosphatidylinositol phosphate analysis. Here we improved upon current methods by enabling the sensitive and simultaneous analysis of phosphatidylinositol and phosphatidylinositol phosphate species, whilst enhancing their characterization through chromatographic resolution between isomeric species. A 1 mM ammonium bicarbonate and ammonia buffer was determined optimal for this goal, enabling the identification of 148 phosphatidylinositide species, including 23 lyso‐phosphatidylinositols, 51 phosphatidylinositols, 59 oxidized‐phosphatidylinositols, and 15 phosphatidylinositol phosphates. As a result of this analysis, four distinct canola cultivars were differentiated based exclusively on their unique phosphatidylinositide‐lipidome, indicating analyses of this type may be of use when considering the development and progression of the disease through lipidomic profiles.

Gertner, DS, Violi, JP, Bishop, DP & Padula, MP 2023, 'Lipid Spectrum Generator: A Simple Script for the Generation of Accurate In Silico Lipid Fragmentation Spectra', Analytical Chemistry, vol. 95, no. 5, pp. 2909-2916.
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Due to the complexity of lipids in nature, the use of in silico generated spectral libraries to identify lipid species from mass spectral data has become an integral part of many lipidomic workflows. However, many in silico libraries are either limited in usability or their capacity to represent lipid species. Here, we introduce Lipid Spectrum Generator, an open-source in silico spectral library generator specifically designed to aid in the identification of lipids in liquid chromatography-tandem mass spectrometry analysis.

Ghorbanpour, S, Kaitu'u-Lino, TJ, Hannan, NJ, Tong, S & McClements, L 2023, 'PO6_24. Validation of FKBPL and CD44 as emerging biomarkers for early-onset preeclampsia diagnosis', Pregnancy Hypertension, vol. 33, pp. e40-e40.
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Ghorbanpour, SM, Richards, C, Pienaar, D, Sesperez, K, Aboulkheyr Es., H, Nikolic, VN, Karadzov Orlic, N, Mikovic, Z, Stefanovic, M, Cakic, Z, Alqudah, A, Cole, L, Gorrie, C, McGrath, K, Kavurma, MM, Ebrahimi Warkiani, M & McClements, L 2023, 'A placenta-on-a-chip model to determine the regulation of FKBPL and galectin-3 in preeclampsia', Cellular and Molecular Life Sciences, vol. 80, no. 2.
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AbstractPreeclampsia is a pregnancy-specific cardiovascular disorder, involving significant maternal endothelial dysfunction. Although inappropriate placentation due to aberrant angiogenesis, inflammation and shallow trophoblast invasion are the root causes of preeclampsia, pathogenic mechanisms are poorly understood, particularly in early pregnancy. Here, we first confirm the abnormal expression of important vascular and inflammatory proteins, FK506-binding protein-like (FKBPL) and galectin-3 (Gal-3), in human plasma and placental tissues from women with preeclampsia and normotensive controls. We then employ a three-dimensional microfluidic placental model incorporating human umbilical vein endothelial cells (HUVECs) and a first trimester trophoblast cell line (ACH-3P) to investigate FKBPL and Gal-3 signaling in inflammatory conditions. In human samples, both circulating (n = 17 controls; n = 30 preeclampsia) and placental (n ≥ 6) FKBPL and Gal-3 levels were increased in preeclampsia compared to controls (plasma: FKBPL, p < 0.0001; Gal-3, p < 0.01; placenta: FKBPL, p < 0.05; Gal-3, p < 0.01), indicative of vascular dysfunction in preeclampsia. In our placenta-on-a-chip model, we show that endothelial cells are critical for trophoblast-mediated migration and that trophoblasts effectively remodel endothelial vascular networks. Inflammatory cytokine tumour necrosis factor-α (10 ng/mL) modulates both FKBPL and Gal-3 signaling in conjunction with trophoblast migration and impairs vascular network formation (p < 0.005). Our placenta-on-a-chip recapitulates aspects of inappropriate placental development and vascular dysfunction in preeclampsia.

Gibbs, M, Ross, P, Scanes, E, Gibbs, J, Rotolo‐Ross, R & Parker, L 2023, 'Extending conservation of coastal and oyster reef restoration for First Nations cultural revitalization', Conservation Biology, vol. 37, no. 6, p. e14158.
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Gilchrist, AM, Wu, X, Hawkins, BA, Hibbs, DE & Gale, PA 2023, 'Fluorinated tetrapodal anion transporters', iScience, vol. 26, no. 2, pp. 105988-105988.
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Gladding, JM, Bradfield, LA & Kendig, MD 2023, 'Diet and obesity effects on cue-driven food-seeking: insights from studies of Pavlovian-instrumental transfer in rodents and humans', Frontiers in Behavioral Neuroscience, vol. 17, p. 1199887.
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Our modern environment is said to be obesogenic, promoting the consumption of calorically dense foods and reducing energy expenditure. One factor thought to drive excess energy intake is the abundance of cues signaling the availability of highly palatable foods. Indeed, these cues exert powerful influences over food-related decision-making. Although obesity is associated with changes to several cognitive domains, the specific role of cues in producing this shift and on decision-making more generally, remains poorly understood. Here we review the literature examining how obesity and palatable diets affect the ability of Pavlovian cues to influence instrumental food-seeking behaviors by examining rodent and human studies incorporating Pavlovian-instrumental transfer (PIT) protocols. There are two types of PIT: (a) general PIT that tests whether cues can energize actions elicited in the pursuit of food generally, and (b) specific PIT which tests whether cues can elicit an action that earns a specific food outcome when faced with a choice. Both types of PIT have been shown to be vulnerable to alterations as a result of changes to diet and obesity. However, effects appear to be driven less by increases in body fat and more by palatable diet exposure per se. We discuss the limitations and implications of the current findings. The challenges for future research are to uncover the mechanisms underlying these alterations to PIT, which appear unrelated to excess weight itself, and to better model the complex determinants of food choice in humans.

Gladding, JM, Lingawi, NW, Leung, BK, Kendig, MD, Chieng, BC & Laurent, V 2023, 'High fat diet allows food-predictive stimuli to energize action performance in the absence of hunger, without distorting insulin signaling on accumbal cholinergic interneurons', Appetite, vol. 188, pp. 106769-106769.
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Goh, YF, Røder, HL, Chan, SH, Ismail, MH, Madsen, JS, Lee, KWK, Sørensen, SJ, Givskov, M, Burmølle, M, Rice, SA & McDougald, D 2023, 'Associational Resistance to Predation by Protists in a Mixed Species Biofilm', Applied and Environmental Microbiology, vol. 89, no. 2, p. e0174122.
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Biofilms have been shown to protect bacterial cells from predation by protists. Biofilm studies have traditionally used single species systems, which have provided information on the mechanisms and regulation of biofilm formation and dispersal, and the effects of predation on these biofilms.

Gomila Pelegri, N, Stanczak, AM, Bottomley, AL, Milthorpe, BK, Gorrie, CA, Padula, MP & Santos, J 2023, 'Adipose-Derived Stem Cells Spontaneously Express Neural Markers When Grown in a PEG-Based 3D Matrix', International Journal of Molecular Sciences, vol. 24, no. 15, pp. 12139-12139.
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Neurological diseases are among the leading causes of disability and death worldwide and remain difficult to treat. Tissue engineering offers avenues to test potential treatments; however, the development of biologically accurate models of brain tissues remains challenging. Given their neurogenic potential and availability, adipose-derived stem cells (ADSCs) are of interest for creating neural models. While progress has been made in differentiating ADSCs into neural cells, their differentiation in 3D environments, which are more representative of the in vivo physiological conditions of the nervous system, is crucial. This can be achieved by modulating the 3D matrix composition and stiffness. Human ADSCs were cultured for 14 days in a 1.1 kPa polyethylene glycol-based 3D hydrogel matrix to assess effects on cell morphology, cell viability, proteome changes and spontaneous neural differentiation. Results showed that cells continued to proliferate over the 14-day period and presented a different morphology to 2D cultures, with the cells elongating and aligning with one another. The proteome analysis revealed 439 proteins changed in abundance by >1.5 fold. Cyclic nucleotide 3′-phosphodiesterase (CNPase) markers were identified using immunocytochemistry and confirmed with proteomics. Findings indicate that ADSCs spontaneously increase neural marker expression when grown in an environment with similar mechanical properties to the central nervous system.

Gong, X-W, Leigh, A, Guo, J-J, Fang, L-D & Hao, G-Y 2023, 'Sand dune shrub species prioritize hydraulic integrity over transpirational cooling during an experimental heatwave', Agricultural and Forest Meteorology, vol. 336, pp. 109483-109483.
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Gonzalez de Vega, R, Clases, D, Cunningham, BA, Ganio, K, Neville, SL, McDevitt, CA & Doble, PA 2023, 'Spatial distribution of trace metals and associated transport proteins during bacterial infection', Analytical and Bioanalytical Chemistry.
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Innate immune systems alter the concentrations of trace elements in host niches in response to invading pathogens during infection. This work reports the interplay between d-block metal ions and their associated biomolecules using hyphenated elemental techniques to spatially quantify both elemental distributions and the abundance of specific transport proteins. Here, lung tissues were collected for analyses from naïve and Streptococcus pneumoniae-infected mice fed on a zinc-restricted or zinc-supplemented diet. Spatiotemporal distributions of manganese (55Mn), iron (56Fe), copper (63Cu), and zinc (66Zn) were determined by quantitative laser ablation-inductively coupled plasma-mass spectrometry. The murine transport proteins ZIP8 and ZIP14, which are associated with zinc transport, were also imaged by incorporation of immunohistochemistry techniques into the analytical workflow. Collectively, this work demonstrates the potential of a single instrumental platform suitable for multiplex analyses of tissues and labelled antibodies to investigate complex elemental interactions at the host-pathogen interface. Further, these methods have the potential for broad application to investigations of biological pathways where concomitant measurement of elements and biomolecules is crucial to understand the basis of disease and aid in development of new therapeutic approaches.

Goodswen, SJ, Kennedy, PJ & Ellis, JT 2023, 'A guide to current methodology and usage of reverse vaccinology towardsin silicovaccine discovery', FEMS Microbiology Reviews, vol. 47, no. 2, p. fuad004.
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AbstractReverse vaccinology (RV) was described at its inception in 2000 as an in silico process that starts from the genomic sequence of the pathogen and ends with a list of potential protein and/or peptide candidates to be experimentally validated for vaccine development. Twenty-two years later, this process has evolved from a few steps entailing a handful of bioinformatics tools to a multitude of steps with a plethora of tools. Other in silico related processes with overlapping workflow steps have also emerged with terms such as subtractive proteomics, computational vaccinology, and immunoinformatics. From the perspective of a new RV practitioner, determining the appropriate workflow steps and bioinformatics tools can be a time consuming and overwhelming task, given the number of choices. This review presents the current understanding of RV and its usage in the research community as determined by a comprehensive survey of scientific papers published in the last seven years. We believe the current mainstream workflow steps and tools presented here will be a valuable guideline for all researchers wanting to apply an up-to-date in silico vaccine discovery process.

Goodswen, SJ, Kennedy, PJ & Ellis, JT 2023, 'A state-of-the-art methodology for high-throughput in silico vaccine discovery against protozoan parasites and exemplified with discovered candidates for Toxoplasma gondii', Scientific Reports, vol. 13, no. 1, p. 8243.
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AbstractVaccine discovery against eukaryotic parasites is not trivial as highlighted by the limited number of known vaccines compared to the number of protozoal diseases that need one. Only three of 17 priority diseases have commercial vaccines. Live and attenuated vaccines have proved to be more effective than subunit vaccines but adversely pose more unacceptable risks. One promising approach for subunit vaccines is in silico vaccine discovery, which predicts protein vaccine candidates given thousands of target organism protein sequences. This approach, nonetheless, is an overarching concept with no standardised guidebook on implementation. No known subunit vaccines against protozoan parasites exist as a result of this approach, and consequently none to emulate. The study goal was to combine current in silico discovery knowledge specific to protozoan parasites and develop a workflow representing a state-of-the-art approach. This approach reflectively integrates a parasite’s biology, a host's immune system defences, and importantly, bioinformatics programs needed to predict vaccine candidates. To demonstrate the workflow effectiveness, every Toxoplasma gondii protein was ranked in its capacity to provide long-term protective immunity. Although testing in animal models is required to validate these predictions, most of the top ranked candidates are supported by publications reinforcing our confidence in the approach.

Goulden, T, Bodachivskyi, I, Padula, MP & Williams, DBG 2023, 'Concentrated ionic liquids for proteomics: Caveat emptor!', International Journal of Biological Macromolecules, vol. 253, pp. 127438-127438.
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Gow, I, Smith, N, Stark, D & Ellis, J 2023, 'Molecular Detection of Neglected Tropical Diseases: The Case for Automated Near–Point-of-Care Diagnosis of Leishmaniasis', The American Journal of Tropical Medicine and Hygiene, vol. 108, no. 1, pp. 2-6.
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ABSTRACT.Neglected tropical diseases affect those in poorer nations disproportionately across the globe. One example of these, leishmaniasis, is a debilitating and potentially fatal parasitic infection. Molecular detection of this disease can provide accurate and fast diagnosis, and with near point-of-care technologies, detection can be provided in many health-care settings. Traditionally, the perceived limitations to such detection methods have hindered their provision to resource-limited nations, but new technologies and techniques are helping to overcome these perceptions. The current pandemic offers an opportunity to maintain and develop further advances, ensuring molecular diagnostics are accessible to all.

Gray, JM, Leys, JF, Yang, X & Zhang, M 2023, 'Monitoring of sustainable land management using remotely sensed vegetation cover and variable tolerable soil erosion targets across New South Wales, Australia', Soil Use and Management, vol. 39, no. 2, pp. 849-866.
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AbstractThe monitoring of land management practices is vital for the protection of soil resource and the environment. Here, we present a new approach to monitor sustainable land management using widely available remotely sensed data, such as MODIS fractional vegetation cover data. The method is based on the concept of maintaining sufficient vegetation cover to prevent hillslope water erosion beyond tolerable soil erosion targets. The targets were based on long‐term natural erosion rates plus a small constant and are spatially and temporally variable, not static as in most reported studies to date. Where vegetation cover is more than that required to prevent nontolerable erosion under normal conditions for that calendar month, the site (pixel) is deemed to be managed sustainably. Monthly indices are then combined to form a yearly sustainable land management index (SLMI), presented as raster maps with a spatial resolution of 100 m. We explored this new method through case studies over New South Wales (NSW), Australia, over the period 2010 to 2021, with a particular examination of 2020. Results were further stratified by land uses and natural resource management regions, which revealed useful data and trends. The method is offered as an example of the potential use of readily available vegetation cover data to quantitatively assess and monitor levels of sustainable land management across landscapes. We believe it overcomes the limitations of previous methods to monitor vegetation cover and land management from remote‐sensed data alone. Other users are encouraged to adapt the broad approach to meet local requirements.

Griebel, A, Boer, MM, Blackman, C, Choat, B, Ellsworth, DS, Madden, P, Medlyn, B, Resco de Dios, V, Wujeska‐Klause, A, Yebra, M, Younes Cardenas, N & Nolan, RH 2023, 'Specific leaf area and vapour pressure deficit control live fuel moisture content', Functional Ecology, vol. 37, no. 3, pp. 719-731.
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AbstractThe live fuel moisture content (LFMC) is an important precondition for wildfire activity, yet it remains challenging to predict LFMC due to the dynamic interplay between atmospheric and hydrological conditions that determine the plant's access to, and loss of water.We monitored LFMC and a range of plant water‐use traits (predawn and midday leaf water potentials [Ψleaf]), leaf traits (specific leaf area [SLA]), hydrological status (soil water content [SWC] in the shallow layer and full profile) and atmospheric variables (air temperature, vapour pressure deficit [VPD], CO2 concentrations) in a mature eucalypt woodland at the Eucalyptus Free‐Air CO2 Enrichment (EucFACE) facility during a drought.We combined plant traits, hydrological status and atmospheric variables into a biophysical model to predict LFMC dynamics, and compared these with predictions of LFMC based on a satellite model and established relationships between Ψleaf and LFMC from pressure–volume curves.Predawn Ψleaf could be well predicted from changes in SWC, but variation in midday Ψleaf and LFMC were more responsive to atmospheric than hydrological variables. The biophysical model explained up to 89% of variability in LFMC and outperformed established approaches to predict LFMC. SLA was the single most important variable to predict LFMC, followed by VPD, which explained 33% of the remaining variability in LFMC.Our study demonstrates that the co‐variation of plant traits and atmospheric and hydrological conditions affect LFMC during drought, suggesting a new w...

Gu, H, Lam, HC, Pham, TTT & Zinder, Y 2023, 'Heuristics and meta-heuristic to solve the ROADEF/EURO challenge 2020 maintenance planning problem', Journal of Heuristics, vol. 29, no. 1, pp. 139-175.
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Gu, Y, Gu, C, Zhang, Y, Mu, Z & Liu, X 2023, 'Mastering lanthanide energy states for next-gen photonic innovation', Science China Chemistry, vol. 66, no. 9, pp. 2460-2479.
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Guan, P, Min, J, Chen, F, Zhang, S, Hu, L, Ma, Z, Han, Z, Zhou, L, Jia, H, Liu, Y, Sharma, N, Su, D, Hart, JN, Wan, T & Chu, D 2023, 'Enhancing the Electrochemical Properties of Nickel-Rich Cathode by Surface Coating with Defect-Rich Strontium Titanate', ACS Applied Materials & Interfaces, vol. 15, no. 24, pp. 29308-29320.
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Guan, P, Min, J, Chen, F, Zhang, S, Zhu, Y, Liu, C, Hu, Y, Wan, T, Li, M, Liu, Y, Su, D, Hart, JN, Li, Z & Chu, D 2023, 'Dual-modification of Ni-rich cathode materials through strontium titanate coating and thermal treatment', Journal of Colloid and Interface Science, vol. 652, pp. 1184-1196.
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Gull, N, Arshad, F, Naikoo, GA, Hassan, IU, Pedram, MZ, Ahmad, A, Aljabali, AAA, Mishra, V, Satija, S, Charbe, N, Negi, P, Goyal, R, Serrano-Aroca, Á, Al Zoubi, MS, El-Tanani, M & Tambuwala, MM 2023, 'Recent Advances in Anticancer Activity of Novel Plant Extracts and Compounds from Curcuma longa in Hepatocellular Carcinoma', Journal of Gastrointestinal Cancer, vol. 54, no. 2, pp. 368-390.
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Abstract Purpose Among all forms of cancers, hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. There are several treatment options for HCC ranging from loco-regional therapy to surgical treatment. Yet, there is high morbidity and mortality. Recent research focus has shifted towards more effective and less toxic cancer treatment options. Curcumin, the active ingredient in the Curcuma longa plant, has gained widespread attention in recent years because of its multifunctional properties as an antioxidant, anti-inflammatory, antimicrobial, and anticancer agent. Methods A systematic search of PubMed, Embase and Google Scholar was performed for studies reporting incidence of HCC, risk factors associated with cirrhosis and experimental use of curcumin as an anti-cancer agent. Results This review exclusively encompasses the anti-cancer properties of curcumin in HCC globally and it’s postulated molecular targets of curcumin when used against liver cancers. Conclusions This review is concluded by presenting the current challenges and future perspectives of novel plant extracts derived from C. longa and the treatment options against cancers.

Gunton, H, Fowler, AM, Miller, ME, Booth, DJ & Stewart, J 2023, 'The utility of otolith-based methods for discriminating stock structure of the fishery important monacanthid, Nelusetta ayraud, over an intermediate scale', Fisheries Research, vol. 264, pp. 106715-106715.
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Gupta, S, Deb Burman, PK, Tiwari, YK, Dumka, UC, Kumari, N, Srivastava, A & Raghubanshi, AS 2023, 'Understanding carbon sequestration trends using model and satellite data under different ecosystems in India', Science of The Total Environment, vol. 897, pp. 166381-166381.
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This study discusses carbon sequestration variability in different ecosystems of India. Four different biosphere regions, each over 0.5° × 0.5° area, have been selected considering the geospatial and climatic variability of these regions expanding from Central India (CI), the Northeast region (NER), the Western Ghats (WG), and the Western Himalayan region (WHNI). The climatic conditions of these four regions are different so are the biosphere constituents of these regions. We expect the Gross Primary Productivity (GPP) to enhance during the all India summer monsoon rainfall season but in varied magnitudes suggesting a role of climatic parameters and flora in these regions. The GPP from FLUXCOM for the duration of 2001 to 2019 (19 years) and satellite-derived vegetation indices like the Normalized Vegetation Index (NDVI), Enhanced Vegetation Index (EVI), and Leaf Area Index (LAI) are used in this study to understand the response of regional vegetation to this variability. EVI seems to be better related to GPP in comparison to NDVI in the preliminary analysis. Further analysis suggests LAI correlates better to GPP than EVI and NDVI in different seasons in these four regions. Also, meteorological parameters like surface temperature, rainfall, soil water, and other derived parameters like Vapor Pressure Deficit (VPD) are studied. It is also observed that the year-to-year variability in the climatic conditions could also have a role to play in the observed features. It is proven that the climate around the world is experiencing changes. Vegetation is one of the potent markers to monitor the impact of climate change. These long-term data and trends were studied to understand if there is any significant impact of the changing climatic conditions on the vegetation in these regions. Our study shows that there is an increasing (positive) trend in GPP at these locations though at different rates. WG and WHNI have shown a significant high rate of increase (6.44 and...

Haider, MN, Khan, AZ, Usman, M, Balakrishnan, D, Javed, MR, Malik, S, Liu, C-G, Mehmood, MA & Ashraf, GA 2023, 'Impact of seasons and wastewater cultivation on the biomass and biodiesel production by the Plectonema terebrans BERC10 as a candidate for a multiproduct algal biorefinery', Fuel, vol. 332, pp. 125987-125987.
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Cyanobacteria offer efficient resource recovery and biotransformation of the wastewater-derived nutrients into valuable bioproducts. However, to achieve commercial robustness, the cultivation potential of the strain must be evaluated under outdoor conditions. The present study evaluated the potential of a filamentous cyanobacterium Plectonema terebrans BERC10 for resource recovery, wastewater treatment, and biomass production for the whole year using an outdoor open-pond cultivation system. The seasonal and nutrient variations had a strong impact on metabolites and biomass production. Accordingly, the maximum biomass production of 1.9 g/L was produced during the summer season (34–42 °C) while 1.7 g/L, 1.554 g/L, and 1.526 g/L biomass was produced during spring, fall, and winter, respectively. The strain adjusted the pH of the wastewater from 7.5 to 11, offering contamination-free cultivation with easier floatation-based harvesting due to its filamentous nature. Besides, wastewater-based outdoor cultivation diverted the metabolic fluxes towards lipid biosynthesis where it accumulated 50–63 % lipids throughout the year. In addition, a maximum of 21 % carbohydrate content was observed during the summer season, while 9.2 %, 13.11 %, and 17 % were measured in the winter, spring, and fall seasons, respectively. The 16–27 % protein content was achieved throughout the year which was shown to be correlated with the varying nitrogen concentration during different seasons. The biomass produced during all four seasons was separately subjected to cascading processing to make the process cost-effective, and 60 % lipids and 25 % proteins were recovered while the residual biomass contained fermentable carbohydrates. Moreover, the strain showed a promising wastewater treatment potential by lowering the total nitrogen by 90 %, total phosphorus by 99 %, total dissolved solids by 70 %, COD by 80 %, and BOD by 85 %. In conclusion, it exhibited remarkable adaptability to the fluctuati...

Haifer, C, Luu, LDW, Paramsothy, S, Borody, TJ, Leong, RW & Kaakoush, NO 2023, 'Microbial determinants of effective donors in faecal microbiota transplantation for UC', Gut, vol. 72, no. 1, pp. 90-100.
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ObjectiveFaecal microbiota transplantation (FMT) has variable efficacy in treating UC. Recently, oral lyophilised FMT was found to induce remission in patients with UC, with one donor having 100% efficacy compared with a second donor (36% efficacy). We characterised differences in the gut microbiota of these two donors with the aim of improving FMT donor selection.DesignFaecal samples from the two donors were collected over a period of 44 (donor 1) or 70 (donor 2) weeks. The microbiome and metabolome were profiled using shotgun metagenomics and untargeted metabolomicsResultsGut microbiome long-term stability was highly evident in the effective donor. Donor microbiota species evenness was a robust feature associated with clinical efficacy across two clinical trials of FMT in UC, leading to increased donor species engraftment in patients. Alpha diversity and beta diversity of donor gut microbiotas significantly differed. 90 bacterial species and one archaeon were differentially abundant between donors, 44 of which were >0.1% in relative abundance. 17/44 species were enriched in the effective donor, 11 of which (64.7%) were assembled into high-quality genomes that were prevalent (≥75% samples) in that donor, and six showed evidence of engraftment in patients. Taxonomic differences between donors translated to substantial microbial functional differences that were validated using metabolomics.ConclusionDonor microbiota stability and species evenness were identified as novel metrics that were associated with therapeutic efficacy in UC, beyond individual microbial species or metabolites. These metrics may represent community resilience that translates to better engraftment in the host.Tr...

Hamzelou, S, Belobrajdic, D, Broadbent, JA, Juhász, A, Lee Chang, K, Jameson, I, Ralph, P & Colgrave, ML 2023, 'Utilizing proteomics to identify and optimize microalgae strains for high-quality dietary protein: a review', Critical Reviews in Biotechnology, pp. 1-16.
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Algae-derived protein has immense potential to provide high-quality protein foods for the expanding human population. To meet its potential, a broad range of scientific tools are required to identify optimal algal strains from the hundreds of thousands available and identify ideal growing conditions for strains that produce high-quality protein with functional benefits. A research pipeline that includes proteomics can provide a deeper interpretation of microalgal composition and biochemistry in the pursuit of these goals. To date, proteomic investigations have largely focused on pathways that involve lipid production in selected microalgae species. Herein, we report the current state of microalgal proteome measurement and discuss promising approaches for the development of protein-containing food products derived from algae.

Han, N, Zhang, W, Guo, W, Pan, H, Jiang, B, Xing, L, Tian, H, Wang, G, Zhang, X & Fransaer, J 2023, 'Designing Oxide Catalysts for Oxygen Electrocatalysis: Insights from Mechanism to Application', Nano-Micro Letters, vol. 15, no. 1.
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AbstractThe electrochemical oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) are fundamental processes in a range of energy conversion devices such as fuel cells and metal–air batteries. ORR and OER both have significant activation barriers, which severely limit the overall performance of energy conversion devices that utilize ORR/OER. Meanwhile, ORR is another very important electrochemical reaction involving oxygen that has been widely investigated. ORR occurs in aqueous solutions via two pathways: the direct 4-electron reduction or 2-electron reduction pathways from O2 to water (H2O) or from O2 to hydrogen peroxide (H2O2). Noble metal electrocatalysts are often used to catalyze OER and ORR, despite the fact that noble metal electrocatalysts have certain intrinsic limitations, such as low storage. Thus, it is urgent to develop more active and stable low-cost electrocatalysts, especially for severe environments (e.g., acidic media). Theoretically, an ideal oxygen electrocatalyst should provide adequate binding to oxygen species. Transition metals not belonging to the platinum group metal-based oxides are a low-cost substance that could give a d orbital for oxygen species binding. As a result, transition metal oxides are regarded as a substitute for typical precious metal oxygen electrocatalysts. However, the development of oxide catalysts for oxygen reduction and oxygen evolution reactions still faces significant challenges, e.g., catalytic activity, stability, cost, and reaction mechanism. We discuss the fundamental principles underlying the design of oxide catalysts, including the influence of crystal structure, and electronic structure on their performance. We also discuss the challenges associated with developing oxide catalysts and the potential strategies to overcome these challenges.

Han, W, Hu, J, Su, H, Zhang, Q, Sun, B & Fan, L 2023, 'Self-supported Ni2P nanoarrays as efficient electrocatalysts for oxygen evolution reaction and hydrogen evolution reaction', Materials Letters, vol. 351, pp. 134998-134998.
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Hanna, T, Chadwick, S & Moret, S 2023, 'Fingermark quality assessment, a transversal study of subjective quality scales', Forensic Science International, vol. 350, pp. 111783-111783.
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Hansbro, P 2023, 'Omics technologies to study virus infection and chronic lung diseases', Respirology, vol. 28, no. 4, pp. 403-403.
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Hardy, SA, Liesinger, L, Patrick, R, Poettler, M, Rech, L, Gindlhuber, J, Mabotuwana, NS, Ashour, D, Stangl, V, Bigland, M, Murtha, LA, Starkey, MR, Scherr, D, Hansbro, PM, Hoefler, G, Campos Ramos, G, Cochain, C, Harvey, RP, Birner-Gruenberger, R, Boyle, AJ & Rainer, PP 2023, 'Extracellular Matrix Protein-1 as a Mediator of Inflammation-Induced Fibrosis After Myocardial Infarction', JACC: Basic to Translational Science, vol. 8, no. 12, pp. 1539-1554.
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Harish, V, Mohd, S, Tewari, D, Pandey, NK, Vishwas, S, Babu, MR, Salkini, MA, Rehman, ZU, Alotaibi, JT, Alotaibi, RF, Alrashed, FA, Prasher, P, Sharma, N, Gupta, G, Jakhmola, V, Singh, Y, Pinto, TDJA, Paudel, KR, Mittal, N, Singh, TG, Arora, P, Dua, K & Singh, SK 2023, 'Unravelling the role of solid lipid nanoparticles in drug delivery: Journey from laboratory to clinical trial', Journal of Drug Delivery Science and Technology, vol. 85, pp. 104616-104616.
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Harris, RJ, Bryant, C, Coleman, MA, Leigh, A, Briceño, VF, Arnold, PA & Nicotra, AB 2023, 'A novel and high‐throughput approach to assess photosynthetic thermal tolerance of kelp using chlorophyll α fluorometry', Journal of Phycology, vol. 59, no. 1, pp. 179-192.
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Foundation seaweed species are experiencing widespread declines and localized extinctions due to increased instability of sea surface temperature. Characterizing temperature thresholds are useful for predicting patterns of change and identifying species most vulnerable to extremes. Existing methods for characterizing seaweed thermal tolerance produce diverse metrics and are often time‐consuming, making comparisons between species and techniques difficult, hindering insight into global patterns of change. Using three kelp species, we adapted a high‐throughput method – previously used in terrestrial plant thermal biology – for use on kelps. This method employs temperature‐dependent fluorescence (T–F0) curves under heating or cooling regimes to determine the critical temperature (Tcrit) of photosystem II (PSII), i.e., the breakpoint between slow and fast rise fluorescence response to changing temperature, enabling rapid assays of photosynthetic thermal tolerance using a standardized metric. This method enables characterization of Tcrit for up to 48 samples per two‐hour assay, demonstrating the capacity of T–F0 curves for high‐throughput assays of thermal tolerance. Temperature‐dependent fluorescence curves and their derived metric, Tcrit, may offer a timely and powerful new method for the field of phycology, enabling characterization and comparison of photosynthetic thermal tolerance of seaweeds across many populations, species, and biomes.

Hasoon, MF, Jarocki, VM, Mohammed, MH, Djordjevic, SP, Yip, HYE, Carr, M, Khabiri, A, Azari, AA, Amanollahi, R, Jozani, RJ, Carracher, B, Mollinger, J, Deutscher, AT, Hemmatzadeh, F & Trott, DJ 2023, 'Antimicrobial susceptibility and molecular characteristics of Mycoplasma bovis isolated from cases of bovine respiratory disease in Australian feedlot cattle', Veterinary Microbiology, vol. 283, pp. 109779-109779.
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Hassler, GW, Magee, AF, Zhang, Z, Baele, G, Lemey, P, Ji, X, Fourment, M & Suchard, MA 2023, 'Data Integration in Bayesian Phylogenetics', Annual Review of Statistics and Its Application, vol. 10, no. 1, pp. 353-377.
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Researchers studying the evolution of viral pathogens and other organisms increasingly encounter and use large and complex data sets from multiple different sources. Statistical research in Bayesian phylogenetics has risen to this challenge. Researchers use phylogenetics not only to reconstruct the evolutionary history of a group of organisms, but also to understand the processes that guide its evolution and spread through space and time. To this end, it is now the norm to integrate numerous sources of data. For example, epidemiologists studying the spread of a virus through a region incorporate data including genetic sequences (e.g., DNA), time, location (both continuous and discrete), and environmental covariates (e.g., social connectivity between regions) into a coherent statistical model. Evolutionary biologists routinely do the same with genetic sequences, location, time, fossil and modern phenotypes, and ecological covariates. These complex, hierarchical models readily accommodate both discrete and continuous data and have enormous combined discrete/continuous parameter spaces including, at a minimum, phylogenetic tree topologies and branch lengths. The increasedsize and complexity of these statistical models have spurred advances in computational methods to make them tractable. We discuss both the modeling and computational advances, as well as unsolved problems and areas of active research.

Haydon, TD, Matthews, JL, Seymour, JR, Raina, J-B, Seymour, JE, Chartrand, K, Camp, EF & Suggett, DJ 2023, 'Metabolomic signatures of corals thriving across extreme reef habitats reveal strategies of heat stress tolerance', Proceedings of the Royal Society B: Biological Sciences, vol. 290, no. 1992.
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Anthropogenic stressors continue to escalate worldwide, driving unprecedented declines in reef environmental conditions and coral health. One approach to better understand how corals can function in the future is to examine coral populations that thrive within present day naturally extreme habitats. We applied untargeted metabolomics (gas chromatography–mass spectrometry (GC–MS)) to contrast metabolite profiles of Pocillopora acuta colonies from hot, acidic and deoxygenated mangrove environments versus those from adjacent reefs. Under ambient temperatures, P. acuta predominantly associated with endosymbionts of the genera Cladocopium (reef) or Durusdinium (mangrove), exhibiting elevated metabolism in mangrove through energy-generating and biosynthesis pathways compared to reef populations. Under transient heat stress, P. acuta endosymbiont associations were unchanged. Reef corals bleached and exhibited extensive shifts in symbiont metabolic profiles (whereas host metabolite profiles were unchanged). By contrast, mangrove populations did not bleach and solely the host metabolite profiles were altered, including cellular responses in inter-partner signalling, antioxidant capacity and energy storage. Thus mangrove P. acuta populations resist periodically high-temperature exposure via association with thermally tolerant endosymbionts coupled with host metabolic plasticity. Our findings highlight specific metabolites that may be biomarkers of heat tolerance, providing novel insight into adaptive coral resilience to elevated temperatures.

He, Q, Liu, DL, Wang, B, Cowie, A, Simmons, A, Waters, C, Li, L, Feng, P, Li, Y, Voil, PD, Huete, A & Yu, Q 2023, 'Modelling interactions between cowpea cover crops and residue retention in Australian dryland cropping systems under climate change', Agriculture, Ecosystems & Environment, vol. 353, pp. 108536-108536.
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Healey, AJ, Scholten, SC, Yang, T, Scott, JA, Abrahams, GJ, Robertson, IO, Hou, XF, Guo, YF, Rahman, S, Lu, Y, Kianinia, M, Aharonovich, I & Tetienne, J-P 2023, 'Quantum microscopy with van der Waals heterostructures', Nature Physics, vol. 19, no. 1, pp. 87-91.
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Hemsley, B, Darcy, S, Given, F, Murray, BR & Balandin, S 2023, 'Going thirsty for the turtles: Plastic straw bans, people with swallowing disability, and Sustainable Development Goal 14, Life Below Water', International Journal of Speech-Language Pathology, vol. 25, no. 1, pp. 15-19.
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Heng, WS, Jadhav, SR, Ueland, M & Shellie, RA 2023, 'Rapid detection of Escherichia coli in dairy milk using static headspace-comprehensive two-dimensional gas chromatography', Analytical and Bioanalytical Chemistry, vol. 415, no. 13, pp. 2535-2545.
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Henry, JA, Szereday, S, Lynn, CK, Suggett, DJ, Camp, EF & Patterson, JT 2023, 'Using relative return‐on‐effort scoring to evaluate a novel coral nursery in Malaysia', Restoration Ecology, vol. 31, no. 3.
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Coral reefs in Malaysia have been degraded by environmental and anthropogenic stressors, and enthusiasm for coral propagation aimed at site restoration is rapidly growing as a local management tool. However, coral propagation activities in the region are in their infancy and little data currently exists to guide and inform effective practices. We therefore established the first multi‐taxa coral tree nursery (6 species and 300 fragments) in Malaysia and tracked survival and growth to determine the relative return‐on‐effort (RRE) over an approximately 14‐month monitoring period. We observed differences in growth and survival among six coral species and were successful at benchmarking results against coral restoration operations globally and in the East Asian Seas region. Major findings include (1) overall ranges in species level survivorship of 34–94% and specific growth rate of 0.14–0.29%/day, leading to variable RRE scores among species, (2) variable growth rates among coral species based on seasonal changes in environmental conditions, (3) similar RRE scores to other nursery locations worldwide, which suggests effective practice, and (4) calculation of RRE scores for species not previously reported in nursery culture (Acropora florida, A. hoeksemai, and Echinopora horrida). Ultimately, our study supports previous findings that RRE is an effective technique for comparing coral nursery performance and offers valuable insight to guide future restoration activities in Malaysia.

Herdean, A, Hall, C, Hughes, DJ, Kuzhiumparambil, U, Diocaretz, BC & Ralph, PJ 2023, 'Temperature mapping of non-photochemical quenching in Chlorella vulgaris', Photosynthesis Research, vol. 155, no. 2, pp. 191-202.
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AbstractLight intensity and temperature independently impact all parts of the photosynthetic machinery in plants and algae. Yet to date, the vast majority of pulse amplitude modulated (PAM) chlorophyll a fluorescence measurements have been performed at well-defined light intensities, but rarely at well-defined temperatures. In this work, we show that PAM measurements performed at various temperatures produce vastly different results in the chlorophyte Chlorella vulgaris. Using a recently developed Phenoplate technique to map quantum yield of Photosystem II (Y(II)) and non-photochemical quenching (NPQ) as a function of temperature, we show that the fast-relaxing NPQ follows an inverse normal distribution with respect to temperature and appears insensitive to previous temperature acclimation. The slow-relaxing or residual NPQ after 5 minutes of dark recovery follows a normal distribution similar to Y(II) but with a peak in the higher temperature range. Surprisingly, higher slow- and fast-relaxing NPQ values were observed in high-light relative to low-light acclimated cultures. Y(II) values peaked at the adaptation temperature regardless of temperature or light acclimation. Our novel findings show the complete temperature working spectrum of Y(II) and how excess energy quenching is managed across a wide range of temperatures in the model microalgal species C. vulgaris. Finally, we draw attention to the fact that the effect of the temperature component in PAM measurements has been wildly underestimated, and results from experiments at room temperature can be misleading.

Hoch, L, Herdean, A, Argyle, PA & Ralph, PJ 2023, 'High throughput phenomics for diatoms: Challenges and solutions', Progress in Oceanography, vol. 216, pp. 103074-103074.
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Hoque, MM, Espinoza-Vergara, G & McDougald, D 2023, 'Protozoan predation as a driver of diversity and virulence in bacterial biofilms', FEMS Microbiology Reviews, vol. 47, no. 4.
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Abstract Protozoa are eukaryotic organisms that play a crucial role in nutrient cycling and maintaining balance in the food web. Predation, symbiosis and parasitism are three types of interactions between protozoa and bacteria. However, not all bacterial species are equally susceptible to protozoan predation as many are capable of defending against predation in numerous ways and may even establish either a symbiotic or parasitic life-style. Biofilm formation is one such mechanism by which bacteria can survive predation. Structural and chemical components of biofilms enhance resistance to predation compared to their planktonic counterparts. Predation on biofilms gives rise to phenotypic and genetic heterogeneity in prey that leads to trade-offs in virulence in other eukaryotes. Recent advances, using molecular and genomics techniques, allow us to generate new information about the interactions of protozoa and biofilms of prey bacteria. This review presents the current state of the field on impacts of protozoan predation on biofilms. We provide an overview of newly gathered insights into (i) molecular mechanisms of predation resistance in biofilms, (ii) phenotypic and genetic diversification of prey bacteria, and (iii) evolution of virulence as a consequence of protozoan predation on biofilms.

Hoque, MM, Noorian, P, Espinoza-Vergara, G, Adhikary, S, To, J, Rice, SA & McDougald, D 2023, 'Increased iron utilization and oxidative stress tolerance in a Vibrio cholerae flrA mutant confers resistance to amoeba predation', Applied and Environmental Microbiology, vol. 89, no. 11, p. e0109523.
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ABSTRACT The flagellar transcriptional regulator flrA initiates the regulatory cascade of flagellum synthesis in Vibrio cholerae . Previously, we observed an increase in sub-populations of V. cholerae carrying mutations in the flrA gene during long-term co-adaptation with the amoeba host Acanthamoeba castellanii . The flrA mutants exhibit increased growth and intracellular survival in the amoeba host but the molecular mechanisms were unknown. Using an in-frame deletion of flrA, here we show that the absence of flrA increases pathogen growth and induces a distinct V. cholerae transcriptomic signature during amoeba predation. Transcriptome analysis of a flrA mutant in A. castellanii revealed that several genes involved in iron acquisition and amino acid biosynthesis are highly up-regulated compared to the wild-type strain. Furthermore, we show that iron availability is crucial for the survival of V. cholerae in amoeba. We also report that V. cholerae KatB and KatG catalases confer an increased tolerance to oxidative stress. We conclude that the increased survival of the flrA mutant in amoeba is due to a combination of factors, including resistance to oxidative stress and an increased capacity to util...

Hossain, KR, Turkewitz, DR, Holt, SA, Le Brun, AP & Valenzuela, SM 2023, 'Sterol Structural Features’ Impact on the Spontaneous Membrane Insertion of CLIC1 into Artificial Lipid Membranes', Langmuir, vol. 39, no. 9, pp. 3286-3300.
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Howlett, L, Camp, EF, Edmondson, J, Hosp, R, Taylor, B, Coulthard, P & Suggett, DJ 2023, 'Active coral propagation outcomes on coral communities at high-value Great Barrier Reef tourism sites', Biological Conservation, vol. 279, pp. 109930-109930.
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Huang, X, Li, F, Wang, Y, Jia, X, Jia, N, Xiao, F, Sun, C, Fu, J, Chen, M, Cui, X, Qu, D, Wai Luu, LD, Tai, J & Li, J 2023, 'Multi-omics analysis reveals underlying host responses in pediatric respiratory syncytial virus pneumonia', iScience, vol. 26, no. 4, pp. 106329-106329.
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Respiratory syncytial virus (RSV) is an important pathogen causing pneumonia in children. Few studies have used multi-omics data to investigate the pathogenies of RSV pneumonia. Here, metabolomics was first used to identify potential biomarkers for RSV diagnosis. In the training cohort, serum from 36 healthy controls (HCs), 45 RSV pneumonia children, and 32 infectious disease controls (IDCs) were recruited. After analyses, six metabolites had potential diagnostic value. Using an independent cohort of 49 subjects, two biomarkers (neuromedin N and histidyl-proline diketopiperazine) were validated. Next, multi-omics analysis were applied to analyze the pathogenies of RSV pneumonia. Accumulation of collagen in the serum of RSVs indicated that RSV infection could lead to increased levels of soluble collage. Activation of the complement system and imbalance in lipid metabolism were also observed in RSV patients. The multi-omics analysis presented here revealed the signature protein and metabolite changes in serum caused by RSV infection.

Huang, Y, Du, Z, Bao, G, Fang, G, Cappadona, M, McClements, L, Tuch, BE, Lu, H & Xu, X 2023, 'Smart Drug-Delivery System of Upconversion Nanoparticles Coated with Mesoporous Silica for Controlled Release', Pharmaceutics, vol. 15, no. 1, pp. 89-89.
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Drug-delivery vehicles have garnered immense interest in recent years due to unparalleled progress made in material science and nanomedicine. However, the development of stimuli-responsive devices with controllable drug-release systems (DRSs) is still in its nascent stage. In this paper, we designed a two-way controlled drug-release system that can be promoted and prolonged, using the external stimulation of near-infrared light (NIR) and protein coating. A hierarchical nanostructure was fabricated using upconversion nanoparticles (UCNPs)—mesoporous silica as the core-shell structure with protein lysozyme coating. The mesoporous silica shell provides abundant pores for the loading of drug molecules and a specific type of photosensitive molecules. The morphology and the physical properties of the nanostructures were thoroughly characterized. The results exhibited the uniform core-shell nanostructures of ~four UCNPs encapsulated in one mesoporous silica nanoparticle. The core-shell nanoparticles were in the spherical shape with an average size of 200 nm, average surface area of 446.54 m2/g, and pore size of 4.6 nm. Using doxorubicin (DOX), a chemotherapy agent as the drug model, we demonstrated that a novel DRS with capacity of smart modulation to promote or inhibit the drug release under NIR light and protein coating, respectively. Further, we demonstrated the therapeutic effect of the designed DRSs using breast cancer cells. The reported novel controlled DRS with dual functionality could have a promising potential for chemotherapy treatment of solid cancers.

Huang, Z, Jaumaux, P, Sun, B, Guo, X, Zhou, D, Shanmukaraj, D, Armand, M, Rojo, T & Wang, G 2023, 'High-Energy Room-Temperature Sodium–Sulfur and Sodium–Selenium Batteries for Sustainable Energy Storage', Electrochemical Energy Reviews, vol. 6, no. 1.
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AbstractRechargeable room-temperature sodium–sulfur (Na–S) and sodium–selenium (Na–Se) batteries are gaining extensive attention for potential large-scale energy storage applications owing to their low cost and high theoretical energy density. Optimization of electrode materials and investigation of mechanisms are essential to achieve high energy density and long-term cycling stability of Na–S(Se) batteries. Herein, we provide a comprehensive review of the recent progress in Na–S(Se) batteries. We elucidate the Na storage mechanisms and improvement strategies for battery performance. In particular, we discuss the advances in the development of battery components, including high-performance sulfur cathodes, optimized electrolytes, advanced Na metal anodes and modified separators. Combined with current research achievements, this review outlines remaining challenges and clear research directions for the future development of practical high-performance Na–S(Se) batteries. Graphic Abstract

Huang, Z, Wang, S, Guo, X, Safaei, J, Lei, Y, Lai, W, Zhang, X, Sun, B, Shanmukaraj, D, Armand, M, Rojo, T & Wang, G 2023, 'A Hierarchical Hybrid MXenes Interlayer with Triple Function for Room‐Temperature Sodium‐Sulfur Batteries', Advanced Materials Technologies, vol. 8, no. 14.
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AbstractRoom temperature sodium sulfur (RT Na‐S) batteries with high theoretical energy density and low cost have recently gained extensive attention for potential large‐scale energy storage applications. However, the shuttle effect of sodium polysulfides is still the main challenge that leads to poor cycling stability, which hinders the practical application of RT Na‐S batteries. Herein, a multifunctional hybrid MXene interlayer is designed to stabilize the cycling performance of RT Na‐S batteries. The hybrid MXene interlayer comprises a large‐sized Ti3C2Tx nanosheets inner layer followed by a small‐sized Mo2Ti2C3Tx nanoflake outer layer on the surface of the glass fiber (GF) separator. The large‐sized Ti3C2Tx nanosheet inner layer provides an effective physical block and chemical confinement for the soluble polysulfides. The small‐sized Mo2Ti2C3Tx outer layer offers an excellent polysulfide trapping capability and accelerates the reaction kinetics of polysulfide conversion, due to its superior electronic conductivity, large specific surface area, and Mo‐rich catalytic surfaces. As a result, RT Na‐S batteries with this hybrid MXene interlayer modified glass fiber separator deliver a stable cycling performance over 200 cycles at 1 C with an enhanced capacity retention of 71%. This unique structure design provides a novel strategy to develop 2D material‐based functional interlayer for high‐performance metal‐sulfur batteries.

Huston, WM 2023, 'Molecular-viability testing and antimicrobial resistance in sexually transmitted infections', The Lancet Infectious Diseases, vol. 23, no. 10, pp. e399-e399.
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Idrees, S, Paudel, KR, Sadaf, T & Hansbro, PM 2023, 'How different viruses perturb host cellular machinery via short linear motifs.', EXCLI J, vol. 22, pp. 1113-1128.
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The virus interacts with its hosts by developing protein-protein interactions. Most viruses employ protein interactions to imitate the host protein: A viral protein with the same amino acid sequence or structure as the host protein attaches to the host protein's binding partner and interferes with the host protein's pathways. Being opportunistic, viruses have evolved to manipulate host cellular mechanisms by mimicking short linear motifs. In this review, we shed light on the current understanding of mimicry via short linear motifs and focus on viral mimicry by genetically different viral subtypes by providing recent examples of mimicry evidence and how high-throughput methods can be a reliable source to study SLiM-mediated viral mimicry.

Ikram, M & Mahmud, MAP 2023, 'Advanced triboelectric nanogenerator-driven drug delivery systems for targeted therapies', Drug Delivery and Translational Research, vol. 13, no. 1, pp. 54-78.
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Ikram, M, Ilyas, B, Haider, A, Haider, J, Ul‐Hamid, A, Shahzadi, A, Goumri‐Said, S, Kanoun, MB, Nabgan, W & Mahmood, A 2023, 'Fabrication of La‐Doped MoS₂ Nanosheets with Tuned Bandgap for Dye Degradation and Antimicrobial Activities, Experimental and Computational Investigations', Advanced Materials Interfaces, vol. 10, no. 14.
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AbstractThe development of efficient catalysts with a large number of active sites, tunable bandgap, and large surface area has been very challenging. In addition, a significant bottleneck in the application of catalysts for water treatment is their dissolution under extreme conditions, such as highly acidic or highly alkaline conditions that lead to poor application of the reported materials in real‐world applications. In this study, the lanthanum (La)‐doped molybdenum disulfide (MoS2) nanosheets are reported for efficient breakdown of toxic pollutants from wastewater under a wide pH range from strongly alkaline to strongly acidic solutions. The La‐MoS2 nanosheets (NSs) are prepared by a facile hydrothermal approach using a two‐step methodology. A redshift is observed upon La doping, indicating that the bandgap is lowered after La doping in MoS2. The changes in bandgap and electronic structure are further investigated using the density functional theory (DFT), which reveal that doping of La introduces new states within the bandgap region, allowing for further induced energy transitions. The La‐MoS2, having a doping concentration of 2%, exhibits the highest catalytic activity against methylene blue (MB) in neutral, acidic, and alkaline solutions, as well as substantial inhibitory activity for bacterial strains such as Escherichia coli (E. coli). In summary, the modified catalyst provides a pathway to design highly efficient catalysts for all pH range water treatment as well as good activity against microbes.

Indigo, NL, Kelly, E, Smith, J, Webb, JK & Phillips, BL 2023, 'Can conditioned taste aversion be deployed at a landscape level to mitigate the impact of invasive cane toads on northern quolls?', Wildlife Research, vol. 50, no. 12, pp. 1046-1057.
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Context Animals can be taught new behaviours to mitigate threatening processes. However, it is yet to be confirmed if such teaching can be deployed in the field. Here we test this possibility using the invasion of cane toads because they are highly toxic novel prey items to many predators across northern Australia. Aims Research has shown that training predators to avoid toads, using conditioned taste aversion (CTA), significantly improves the survival rates of individuals. We sought to determine if deployment of CTA baits, in situ, could reduce cane toad impacts on a mammalian predator, the northern quoll (Dasyurus hallucatus). Methods The work was conducted in the Kimberley, Western Australia, where we treated three quoll populations with training baits from November 2015–November 2017, and kept four populations as controls. We used camera traps and Bayesian hierarchal modelling to estimate the population size of quolls on up to four occasions before, and two occasions after, cane toad arrival. Key results We observed a 65% reduction in quoll population size at control sites and a 94% reduction at treatment sites: a significant effect of aversion training, but in the direction opposite to that expected. Conclusions Two complexities – decay of aversion, and individual variation – together, may explain our result. Our trials indicate that most animals are no longer averse within 120 days post-training. Earlier studies indicating that aversion training lasts longer may have inadvertently observed innate (i.e. genetically based) aversion to cane toads. Another possibility is that our dose rate of thiabendazole within the CTA baits was, in fact, too low; or the result may be an artefact of the non-random assignment of treatment and control groups. Ultimately, there is no way of determining exactly why our outcome occurred without further laboratory/captive trails. Regardless, our study demonstrates a failure of CTA trainin...

Irga, PJ, Morgan, A, Fleck, R & Torpy, FR 2023, 'Phytoremediation of indoor air pollutants from construction and transport by a moveable active green wall system', Atmospheric Pollution Research, vol. 14, no. 10, pp. 101896-101896.
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Ishida, H, John, U, Murray, SA, Bhattacharya, D & Chan, CX 2023, 'Developing model systems for dinoflagellates in the post‐genomic era', Journal of Phycology, vol. 59, no. 5, pp. 799-808.
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AbstractDinoflagellates are a diverse group of eukaryotic microbes that are ubiquitous in aquatic environments. Largely photosynthetic, they encompass symbiotic, parasitic, and free‐living lineages with a broad spectrum of trophism. Many free‐living taxa can produce bioactive secondary metabolites such as biotoxins, some of which cause harmful algal blooms. In contrast, most symbiotic species are crucial for sustaining coral reef health. The year 2023 marked a decade since the first genome data of dinoflagellates became available. The growing genome‐scale resources for these taxa are highlighting their remarkable evolutionary and genomic complexities. Here, we discuss the prospect of developing dinoflagellate models using the criteria of accessibility, tractability, resources, research support, and promise. Moving forward in the post‐genomic era, we argue for the development of fit‐to‐purpose models that tailor to specific biological contexts, and that a one‐size‐fits‐all model is inadequate for encapsulating the complex biology, ecology, and evolutionary history of dinoflagellates.

Jain, SK, Syed, N, Balendhran, S, Abbas, SAT, Ako, RT, Low, MX, Lobo, C, Zavabeti, A, Murdoch, BJ, Gupta, G, Bhaskaran, M, Crozier, KB, Russo, SP, Daeneke, T & Walia, S 2023, 'Atomically Thin Gallium Nitride for High‐Performance Photodetection', Advanced Optical Materials, vol. 11, no. 15.
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AbstractGallium nitride (GaN) technology has matured and commercialised for optoelectronic devices in the ultraviolet (UV) spectrum over the last few decades. Simultaneously, atomically thin materials with unique features have emerged as contenders for device miniaturization. However, the lack of successful techniques to produce ultra‐thin GaN prevents access to these new predicted properties. Here, this important gap is addressed by printing millimeter‐large ultra‐thin GaN nanosheets (NS) (≈1.4 nm) using a simple two‐step process that simultaneously introduces nitrogen point defects. This extends the photoelectrical spectral response from UV (280 nm) to near infrared (NIR) (1080 nm). The GaN‐based photodetectors display excellent figures of merit, having a responsivity (2.72 × 104 A W−1) up to four orders of magnitude higher than the commercial photodetectors at room temperature, despite being 102–103 times thinner. The photodetectors exhibit fast switching, with rise and decay time in the range of microseconds. The state‐of‐the‐art device performance originates from the ultra‐thin nature of GaN NS coupled with nitrogen point vacancies in the synthesis process. This work presents the opportunity to significantly expand the reach of GaN semiconductor technology and may lead to applications in high‐performance miniaturized imaging systems, spectroscopy, communication, and integrated optoelectronic circuits.

Jang, A, Lee, J, Donahue, C, Coggin-Carr, D, Cummings, M, Trinh, K, Lee, MS, Wieland, S, Zaslawski, C, Prokop, L & Shin, JS 2023, 'Perspectives and Ideas to Advance Integrative Medicine and Healthcare: Proceedings of the 4th Annual Jaseng Academic Conference', Perspectives on Integrative Medicine, vol. 2, no. 3, pp. 190-194.
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The 4^th Annual Jaseng Academic conference (August 13, 2023) in Seoul, South Korea, was a pivotal event in the realm of integrative medicine. Cohosted by Jaseng Hospital of Korean Medicine and Michigan State University College of Osteopathic Medicine, over 500 professionals including Korean medicine doctors, medical doctors, doctors of osteopathic medicine, acupuncturists, researchers, and students gathered at the conference. The theme, “Perspectives on Integrative Medicine,” marked a departure from previous conference themes and embraced a multidisciplinary approach to healthcare. The event highlighted the importance of holistic patient care and cross-disciplinary collaboration within healthcare. It offered a comprehensive overview of the current state of integrative medicine approaches in manual medicine, evidence-based acupuncture treatment, and acupuncture research. The Annual Jaseng Academic conference continues to serve as a platform for healthcare professionals to exchange ideas and perspectives, and bridges the gap between diverse medical systems to promote improved patient outcome and wellbeing.

Jaumaux, P, Wang, S, Zhao, S, Sun, B & Wang, G 2023, 'Electrolyte Solvation Structure Design for High Voltage Zinc‐Based Hybrid Batteries', ENERGY & ENVIRONMENTAL MATERIALS, vol. 6, no. 4.
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Zinc (Zn) metal anodes have enticed substantial curiosity for large‐scale energy storage owing to inherent safety, high specific and volumetric energy capacities of Zn metal anodes. However, the aqueous electrolyte traditionally employed in Zn batteries suffers severe decomposition due to the narrow voltage stability window. Herein, we introduce N‐methylformamide (NMF) as an organic solvent and modulate the solvation structure to obtain a stable organic/aqueous hybrid electrolyte for high‐voltage Zn batteries. NMF is not only extremely stable against Zn metal anodes but also reduces the free water molecule availability by creating numerous hydrogen bonds, thereby accommodating high‐voltage Zn‖LiMn2O4 batteries. The introduction of NMF prevented hydrogen evolution reaction and promoted the creation of an F‐rich solid electrolyte interphase, which in turn hampered dendrite growth on Zn anodes. The Zn‖LiMn2O4 full cells delivered a high average Coulombic efficiency of 99.7% over 400 cycles.

Jaya, FR, Brito, BP & Darling, AE 2023, 'Evaluation of recombination detection methods for viral sequencing', Virus Evolution, vol. 9, no. 2.
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Abstract Recombination is a key evolutionary driver in shaping novel viral populations and lineages. When unaccounted for, recombination can impact evolutionary estimations or complicate their interpretation. Therefore, identifying signals for recombination in sequencing data is a key prerequisite to further analyses. A repertoire of recombination detection methods (RDMs) have been developed over the past two decades; however, the prevalence of pandemic-scale viral sequencing data poses a computational challenge for existing methods. Here, we assessed eight RDMs: PhiPack (Profile), 3SEQ, GENECONV, recombination detection program (RDP) (OpenRDP), MaxChi (OpenRDP), Chimaera (OpenRDP), UCHIME (VSEARCH), and gmos; to determine if any are suitable for the analysis of bulk sequencing data. To test the performance and scalability of these methods, we analysed simulated viral sequencing data across a range of sequence diversities, recombination frequencies, and sample sizes. Furthermore, we provide a practical example for the analysis and validation of empirical data. We find that RDMs need to be scalable, use an analytical approach and resolution that is suitable for the intended research application, and are accurate for the properties of a given dataset (e.g. sequence diversity and estimated recombination frequency). Analysis of simulated and empirical data revealed that the assessed methods exhibited considerable trade-offs between these criteria. Overall, we provide general guidelines for the validation of recombination detection results, the benefits and shortcomings of each assessed method, and future considerations for recombination detection methods for the assessment of large-scale viral sequencing data.

Jelocnik, M, White, RT, Clune, T, O’Connell, J, Foxwell, J, Hair, S, Besier, S, Tom, L, Phillips, N, Robbins, A, Bogema, D, Vaz, PK, Legione, AR, Jenkins, C & Jacobson, C 2023, 'Molecular characterisation of the Australian and New Zealand livestock Chlamydia pecorum strains confirms novel but clonal ST23 in association with ovine foetal loss', Veterinary Microbiology, vol. 283, pp. 109774-109774.
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Jha, SK, Imran, M, Jha, LA, Hasan, N, Panthi, VK, Paudel, KR, Almalki, WH, Mohammed, Y & Kesharwani, P 2023, 'A Comprehensive review on Pharmacokinetic Studies of Vaccines: Impact of delivery route, carrier-and its modulation on immune response', Environmental Research, vol. 236, pp. 116823-116823.
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Jiang, T, Li, X, Li, T, Lin, G, Liu, H, Jin, D & Jiang, L 2023, 'Ultra‐Fast Wetting of the Fresh Popcorn', Advanced Functional Materials, vol. 33, no. 14, pp. 2213036-2213036.
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AbstractWithout chewing, the fresh popcorn dissolves immediately upon being put in the mouth. Such good taste decay dramatically with increasing the exposure time in air, especially in humid air. However, the involving mechanism of the saliva wetting the popcorn remains unclear. Here, it is revealed that the ultra‐fast wetting property of the fresh popcorn is the key for its good taste. For the fresh popcorn, the unique 3D throughout micro‐porous structure facilitates capillary flows both in‐plane and off‐plane at micro‐/nano‐ scale, and the water‐soluble crystalized starch further prompts the water spreading, which cooperatively leads to an immediate structural collapse. The unique ultra‐fast wetting of the fresh popcorn is therefore featured as the wetting with dissolving. After cooling down, the crystalized starch changes gradually into an insoluble amorphous state by absorbing water molecule, as is confirmed by the in situ XRD and infrared spectroscopy. As a result, the ultra‐fast wetting decays drastically with prolonging the in‐air exposure time, as well as the taste, which makes immediate cooking vital for the good taste. It is demonstrated that heating can partially restore the ultra‐fast wetting. It is envisioned that the result will inspire the innovative micro‐fabrication of various starch food by engineering the starch crystalline structure.

Johansen, MD, Spaink, HP, Oehlers, SH & Kremer, L 2023, 'Modeling nontuberculous mycobacterial infections in zebrafish', Trends in Microbiology.
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Johnson, L, Lei, P, Waters, L, Padula, MP & Marks, DC 2023, 'Identification of platelet subpopulations in cryopreserved platelet components using multi-colour imaging flow cytometry', Scientific Reports, vol. 13, no. 1, p. 1221.
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AbstractCryopreservation of platelets, at  − 80 °C with 5–6% DMSO, results in externalisation of phosphatidylserine and the formation of extracellular vesicles (EVs), which may mediate their procoagulant function. The phenotypic features of procoagulant platelets overlap with other platelet subpopulations. The aim of this study was to define the phenotype of in vitro generated platelet subpopulations, and subsequently identify the subpopulations present in cryopreserved components. Fresh platelet components (n = 6 in each group) were either unstimulated as a source of resting platelets; or stimulated with thrombin and collagen to generate a mixture of aggregatory and procoagulant platelets; calcium ionophore (A23187) to generate procoagulant platelets; or ABT-737 to generate apoptotic platelets. Platelet components (n = 6) were cryopreserved with DMSO, thawed and resuspended in a unit of thawed plasma. Multi-colour panels of fluorescent antibodies and dyes were used to identify the features of subpopulations by imaging flow cytometry. A combination of annexin-V (AnnV), CD42b, and either PAC1 or CD62P was able to distinguish the four subpopulations. Cryopreserved platelets contained procoagulant platelets (AnnV+/PAC1−/CD42b+/CD62P+) and a novel population (AnnV+/PAC1−/CD42b+/CD62P−) that did not align with the phenotype of aggregatory (AnnV−/PAC1+/CD42b+/CD62P+) or apoptotic (AnnV+/PAC1−/CD42b−/CD62P−) subpopulations. These data suggests that the enhanced haemostatic potential of cryopreserved platelets may be due to the cryo-induced development of procoagulant platelets, and that additional ...

Johnston, NP, Piwczyński, M, Trzeciak, P, Walczak, K & Szpila, K 2023, 'Integration of mitogenomic and morphological data disentangles the systematics of Pollenia and establishes a revised phylogenetic hypothesis for the Polleniidae', Systematic Entomology, vol. 48, no. 2, pp. 296-315.
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AbstractThe Polleniidae (Diptera) are a family of flies best known for species of the genus Pollenia, which overwinter inside human dwellings. Previously divided across the Calliphoridae, Tachinidae and Rhinophoridae, the polleniid genera have only recently been united. Several studies have utilized molecular data to analyse polleniid phylogenetic relationships, although all have suffered from low taxon sampling or insufficient phylogenetic signal in molecular markers. To alleviate these problems, we utilized two automated organellar genome extraction software, GetOrganelle and MitoFinder, to assemble mitogenomes from genome skimming data from 22 representatives of the polleniid genera: Dexopollenia, Melanodexia, Morinia, Pollenia and Xanthotryxus. From these analyses, we provide 14 new mitogenomes for the Polleniidae and perform phylogenetic analyses of 13 protein‐coding mitochondrial genes using both maximum likelihood and Bayesian inference. Subfamilial phylogenetic relationships within the Polleniidae are interrogated and Pollenia is found to form a monophyletic clade sister to Melanodexia, Morinia and Dexopollenia, providing no evidence for the synonymisation of any of these genera. Our topology conflicts with previous morphology‐based cladistic interpretations, with the amentaria, griseotomentosa, semicinerea and viatica species‐groups resolving as non‐monophyletic. We provide support for our topology through analysis of adult morphology and male and female terminalia, while identifying new diagnostic characters for some of the clades of the Pollenia. To test the validity of the current diagnostic morphology in the Pollenii...

Jones, C, Xavier, J, Vartabi Kashanian, S, Nguyen, M, Aharonovich, I & Vollmer, F 2023, 'Time-dependent Mandel Q parameter analysis for a hexagonal boron nitride single photon source', Optics Express, vol. 31, no. 6, pp. 10794-10794.
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The time-dependent Mandel Q parameter, Q(T), provides a measure of photon number variance for a light source as a function of integration time. Here, we use Q(T) to characterise single photon emission from a quantum emitter in hexagonal boron nitride (hBN). Under pulsed excitation a negative Q parameter was measured, indicating photon antibunching at an integration time of 100 ns. For larger integration times Q is positive and the photon statistics become super-Poissonian, and we show by comparison with a Monte Carlo simulation for a three-level emitter that this is consistent with the effect of a metastable shelving state. Looking towards technological applications for hBN single photon sources, we propose that Q(T) provides valuable information on the intensity stability of single photon emission. This is useful in addition to the commonly used g(2)(τ) function for the complete characterisation of a hBN emitter.

Kamiya, Y, Shiraki, S, Mehraj, H, Akter, MA, Takahashi, S, Seki, M, Dennis, ES, Osabe, K & Fujimoto, R 2023, 'The role of epigenetic modifications in the transcriptional regulation of long noncoding RNAs in Brassica rapa vegetables', Acta Horticulturae, no. 1362, pp. 65-70.
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Kang, JWM, Keay, KA, Kendig, MD, Corbit, LH & Mor, D 2023, 'Serotonin and Dopamine Show Different Response Profiles to Acute Stress in the Nucleus Accumbens and Medial Prefrontal Cortex of Rats with Neuropathic Pain', Neurochemical Research, vol. 48, no. 7, pp. 2265-2280.
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AbstractThe ability to adaptively guide behaviour requires the integration of external information with internal motivational factors. Decision-making capabilities can be impaired by acute stress and is often exacerbated by chronic pain. Chronic neuropathic pain patients often present with cognitive dysfunction, including impaired decision-making. The mechanisms underlying these changes are not well understood but may include altered monoaminergic transmission in the brain. In this study we investigated the relationships between dopamine, serotonin, and their metabolites in key brain regions that regulate motivated behaviour and decision-making. The neurochemical profiles of the medial prefrontal cortex, orbital prefrontal cortex, and nucleus accumbens were analysed using HPLC in rats that received a chronic constriction injury (CCI) of the right sciatic nerve and an acute stress (15-min restraint), prior to an outcome devaluation task. CCI alone significantly decreased dopamine but not serotonin concentrations in the medial prefrontal cortex. By contrast, restraint stress acutely increased dopamine in the medial prefrontal cortex, and the nucleus accumbens; and increased serotonin in the medial prefrontal cortex 2 h later. The sustained dopaminergic and serotonergic responses to acute stress highlight the importance of an animal’s ability to mount an effective coping response. In addition, these data suggest that the impact of nerve injury and acute stress on outcome-devaluation occurs independently of dopaminergic and serotonergic transmission in the medial prefrontal cortex, orbital prefrontal cortex and nucleus accumbens of rats.

Kang, Y, Xu, J, Meng, L, Su, Y, Fang, H, Liu, J, Cheng, YY, Jiang, D, Nie, Y & Song, K 2023, '3D bioprinting of dECM/Gel/QCS/nHAp hybrid scaffolds laden with mesenchymal stem cell-derived exosomes to improve angiogenesis and osteogenesis', Biofabrication, vol. 15, no. 2, pp. 024103-024103.
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Abstract Craniofacial bone regeneration is a coupled process of angiogenesis and osteogenesis, which, associated with infection, still remains a challenge in bone defects after trauma or tumor resection. 3D tissue engineering scaffolds with multifunctional-therapeutic properties can offer many advantages for the angiogenesis and osteogenesis of infected bone defects. Hence, in the present study, a microchannel networks-enriched 3D hybrid scaffold composed of decellularized extracellular matrix (dECM), gelatin (Gel), quaterinized chitosan (QCS) and nano-hydroxyapatite (nHAp) (dGQH) was fabricated by an extrusion 3D bioprinting technology. And enlightened by the characteristics of natural bone microstructure and the demands of vascularized bone regeneration, the exosomes (Exos) isolated from human adipose derived stem cells as angiogenic and osteogenic factors were then co-loaded into the desired dGQH20 hybrid scaffold based on an electrostatic interaction. The results of the hybrid scaffolds performance characterization showed that these hybrid scaffolds exhibited an interconnected pore structure and appropriate degradability (>61% after 8 weeks of treatment), and the dGQH20 hybrid scaffold displayed the highest porosity (83.93 ± 7.38%) and mechanical properties (tensile modulus: 62.68 ± 10.29 MPa, compressive modulus: 16.22 ± 3.61 MPa) among the dGQH hybrid scaffolds. Moreover, the dGQH20 hybrid scaffold presented good antibacterial activities (against 94.90 ± 2.44% of Escherichia coli and 95.41 ± 2.65% of Staphylococcus aureus, respectively) as well as excellent hemocompatibility and biocompatibility. Furthermore, the results of applying the Exos to the dGQH20 hybrid scaffold showed that the Exo promoted the cell attachment and proliferation on the scaffold, and also...

Kannaujiya, VK, De Rubis, G, Paudel, KR, Manandhar, B, Chellappan, DK, Singh, SK, MacLoughlin, R, Gupta, G, Xenaki, D, Kumar, P, Hansbro, PM, Oliver, BGG, Wich, PR & Dua, K 2023, 'Anticancer activity of NFκB decoy oligonucleotide-loaded nanoparticles against human lung cancer', Journal of Drug Delivery Science and Technology, vol. 82, pp. 104328-104328.
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Kapellos, TS, Baßler, K, Fujii, W, Nalkurthi, C, Schaar, AC, Bonaguro, L, Pecht, T, Galvao, I, Agrawal, S, Saglam, A, Dudkin, E, Frishberg, A, de Domenico, E, Horne, A, Donovan, C, Kim, RY, Gallego-Ortega, D, Gillett, TE, Ansari, M, Schulte-Schrepping, J, Offermann, N, Antignano, I, Sivri, B, Lu, W, Eapen, MS, van Uelft, M, Osei-Sarpong, C, van den Berge, M, Donker, HC, Groen, HJM, Sohal, SS, Klein, J, Schreiber, T, Feißt, A, Yildirim, AÖ, Schiller, HB, Nawijn, MC, Becker, M, Händler, K, Beyer, M, Capasso, M, Ulas, T, Hasenauer, J, Pizarro, C, Theis, FJ, Hansbro, PM, Skowasch, D & Schultze, JL 2023, 'Systemic alterations in neutrophils and their precursors in early-stage chronic obstructive pulmonary disease', Cell Reports, vol. 42, no. 6, pp. 112525-112525.
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Systemic inflammation is established as part of late-stage severe lung disease, but molecular, functional, and phenotypic changes in peripheral immune cells in early disease stages remain ill defined. Chronic obstructive pulmonary disease (COPD) is a major respiratory disease characterized by small-airway inflammation, emphysema, and severe breathing difficulties. Using single-cell analyses we demonstrate that blood neutrophils are already increased in early-stage COPD, and changes in molecular and functional neutrophil states correlate with lung function decline. Assessing neutrophils and their bone marrow precursors in a murine cigarette smoke exposure model identified similar molecular changes in blood neutrophils and precursor populations that also occur in the blood and lung. Our study shows that systemic molecular alterations in neutrophils and their precursors are part of early-stage COPD, a finding to be further explored for potential therapeutic targets and biomarkers for early diagnosis and patient stratification.

Keen, B, Cawley, A, Reedy, B, Noble, G, Loy, J & Fu, S 2023, '3-Methoxytyrosine as an indicator of dopaminergic manipulation in equine plasma', Journal of Chromatography B, vol. 1220, pp. 123652-123652.
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Kendig, MD, Hasebe, K, Tajaddini, A, Kaakoush, NO, Westbrook, RF & Morris, MJ 2023, 'The Benefits of Switching to a Healthy Diet on Metabolic, Cognitive, and Gut Microbiome Parameters Are Preserved in Adult Rat Offspring of Mothers Fed a High‐Fat, High‐Sugar Diet', Molecular Nutrition & Food Research, vol. 67, no. 1, pp. 2200318-2200318.
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ScopeMaternal obesity increases the risk of health complications in children, highlighting the need for effective interventions. A rat model of maternal obesity to examine whether a diet switch intervention could reverse the adverse effects of an unhealthy postweaning diet is used.Methods and resultsMale and female offspring born to dams fed standard chow or a high‐fat, high‐sugar “cafeteria” (Caf) diet are weaned onto chow or Caf diets until 22 weeks of age, when Caf‐fed groups are switched to chow for 5 weeks. Adiposity, gut microbiota composition, and place recognition memory are assessed before and after the switch. Body weight and adiposity fall in switched groups but remain significantly higher than chow‐fed controls. Nonetheless, the diet switch improves a deficit in place recognition memory observed in Caf‐fed groups, increases gut microbiota species richness, and alters β diversity. Modeling indicate that adiposity most strongly predicts gut microbiota composition before and after the switch.ConclusionMaternal obesity does not alter the effects of switching diet on metabolic, microbial, or cognitive measures. Thus, a healthy diet intervention lead to major shifts in body weight, adiposity, place recognition memory, and gut microbiota composition, with beneficial effects preserved in offspring born to obese dams.

Kendig, MD, Leigh, S, Hasebe, K, Kaakoush, NO, Westbrook, RF & Morris, MJ 2023, 'Obesogenic Diet Cycling Produces Graded Effects on Cognition and Microbiota Composition in Rats', Molecular Nutrition & Food Research, vol. 67, no. 12.
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ScopeThe effects of diet cycling on cognition and fecal microbiota are not well understood.Method and ResultsAdult male Sprague‐Dawley rats were cycled between a high‐fat, high‐sugar “cafeteria” diet (Caf) and regular chow. The impairment in place recognition memory produced by 16 days of Caf diet was reduced by switching to chow for 11 but not 4 days. Next, rats received 16 days of Caf diet in 2, 4, 8, or 16‐day cycles, each separated by 4‐day chow cycles. Place recognition memory declined from baseline in all groups and was impaired in the 16‐ versus 2‐day group. Finally, rats received 24 days of Caf diet continuously or in 3‐day cycles separated by 2‐ or 4‐day chow cycles. Any Caf diet access impaired cognition and increased adiposity relative to controls, without altering hippocampal gene expression. Place recognition and adiposity were the strongest predictors of global microbiota composition. Overall, diets with higher Caf > chow ratios produced greater spatial memory impairments and larger shifts in gut microbiota species richness and beta diversity.ConclusionResults suggest that diet‐induced cognitive deficits worsen in proportion to unhealthy diet exposure, and that shifting to a healthy chow for at least a week is required for recovery under the conditions tested here.

Kermani, N, Versi, A, Gay, A, Vlasma, J, Jayalatha, AKS, Koppelman, GH, Nawijn, M, Faiz, A, van den Berge, M, Adcock, IM & Chung, KF 2023, 'Gene signatures in U-BIOPRED severe asthma for molecular phenotyping and precision medicine: time for clinical use', Expert Review of Respiratory Medicine, vol. 17, no. 11, pp. 965-971.
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Khan, F, Malik, S, Shahid, A, Siddiqui, AJ, Musharraf, SG, Zhu, H, Alkhattabi, NA, Gull, M & Mehmood, MA 2023, 'Characterization of a newly isolated cyanobacterium Trichocoleus desertorum BERC08 as a potential feedstock for the algal biorefinery', Biomass Conversion and Biorefinery, vol. 13, no. 6, pp. 5283-5294.
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Cyanobacteria have numerous biotechnological applications in the environment, industry, pharmaceutics, food, feed, and energy which is why future cascading biorefineries are believed to employ cyanobacteria as their feedstock. The present study evaluated the potential of a newly isolated cyanobacterium for its applications in the multiproduct biorefinery. Based on morphology and the gene sequence of 23S rRNA, the strain was identified as Trichocoleus desertorum. Various abiotic growth factors including light, pH, and nutrients were optimized to achieve enhanced biomass production using various wastewaters as low-cost growth media. Accordingly, a 2.24-fold to 6.97-fold higher biomass production (gL-1) and biomass productivity of 0.86 gL-1d-1 with a CO2 fixation rate of 1.576 gL-1d-1 was achieved when cultured in synthetic wastewater. Besides, the impact of wastewater cultivation was studied on the biosynthesis of valuable metabolites including proteins, carbohydrates, lipids, and pigments. Accordingly, the lipid content of the wastewater-cultivated strain was increased from 24 to 30%, and protein content was increased from 27 to 46%. The lipids were trans-esterified to biodiesel which was turned out to be good quality biodiesel, as revealed through GC-MS analysis. Additionally, the wastewater-cultivated strain produced 117.35 mgg-1 (11.73 % of the total dried biomass) of phycobilin in response to nutrient manipulation, where phycocyanin was shown to be the most prominent pigment with a yield of 94.7 mgg-1, which covered 80% of the total pigments. These remarkable features reflected the promising potential of this strain to be employed as a feedstock in the multiproduct biorefinery.

Khan, K, Tareen, AK, Iqbal, M, Ye, Z, Xie, Z, Mahmood, A, Mahmood, N & Zhang, H 2023, 'Recent Progress in Emerging Novel MXenes Based Materials and their Fascinating Sensing Applications', Small, vol. 19, no. 19, pp. 2206147-2206147.
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AbstractEarly transition metals based 2D carbides, nitrides and carbonitrides nanomaterials are known as MXenes, a novel and extensive new class of 2D materials family. Since the first accidently synthesis based discovery of Ti3C2in 2011, more than 50 additional compositions have been experimentally reported, including at least eight distinct synthesis methods and also more than 100 stoichiometries are theoretically studied. Due to its distinctive surface chemistry, graphene like shape, metallic conductivity, high hydrophilicity, outstanding mechanical and thermal properties, redox capacity and affordable with mass‐produced nature, this diverse MXenes are of tremendous scientific and technological significance. In this review, first we'll come across the MXene based nanomaterials possible synthesis methods, their advantages, limitations and future suggestions, new chemistry related to their selected properties and potential sensing applications, which will help us to explain why this family is growing very fast as compared to other 2D families. Secondly, problems that help to further improve commercialization of the MXene nanomaterials based sensors are examined, and many advances in the commercializing of the MXene nanomaterials based sensors are proposed. At the end, we'll go through the current challenges, limitations and future suggestions.

Kim, JH, Ajani, PA, Murray, SA, Kang, S-M, Kim, S-H, Lim, HC, Teng, ST, Lim, PT & Park, BS 2023, 'Abiotic and biotic factors controlling sexual reproduction in populations of Pseudo-nitzschia pungens (Bacillariophyceae)', Harmful Algae, vol. 123, pp. 102392-102392.
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Pseudo-nitzschia pungens is a widely distributed marine pennate diatom. Hybrid zones, regions in which two different genotypes may interbreed, are important areas for speciation and ecology, and have been reported across the globe for this species. However, sexual reproduction between differing clades in the natural environment is yet to be observed and is difficult to predict. Here we carried out experiments using two mono-clonal cultures of P. pungens from different genotypes to measure the frequency and timing of sexual reproduction across varying biotic (growth phases and cell activity potential) and abiotic conditions (nutrients, light, turbulence). We found the mating rates and number of zygotes gradually decreased from exponential to late stationary growth phases. The maximum zygote abundance observed was 1,390 cells mL-1 and the maximum mating rate was 7.1%, both which occurred during the exponential growth phase. Conversely, only 9 cells mL-1 and a maximum mating rate of 0.1% was observed during the late stationary phase. We also found the higher the relative potential cell activity (rPCA) in parent cells, as determined by the concentration of chlorophyll a per cell and the ratio of colony formation during parent cultivations, revealed higher mating rates. Furthermore, sexual events were reduced under nutrient enrichment conditions, and mating pairs and zygotes were not formed under aphotic (dark) or shaking culture conditions (150 rpm). In order to understand the sexual reproduction of Pseudo-nitzschia in the natural environment, our results highlight that it is most likely the combination of both biotic (growth phase, Chl. a content) and abiotic factors (nutrients, light, turbulence) that will determine the successful union of intraspecific populations of P. pungens in any given region.

Kim, RY & Oliver, B 2023, 'Innate Immune Reprogramming in Chronic Obstructive Pulmonary Disease: New Mechanisms for Old Questions', American Journal of Respiratory Cell and Molecular Biology, vol. 68, no. 5, pp. 470-471.
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Klanten, OS, Gall, M, Barbosa, SS, Hart, MW, Keever, CC, Puritz, JB, Harantio, J, Toonen, RJ, Selvakumaraswamy, P, Grosberg, RK & Byrne, M 2023, 'Population connectivity across east Australia's bioregions and larval duration of the range‐extending sea star Meridiastra calcar', Aquatic Conservation: Marine and Freshwater Ecosystems, vol. 33, no. 10, pp. 1061-1078.
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AbstractThe diversity and distribution of marine species in eastern Australia is influenced by one of the world's strongest western boundary currents, the East Australia Current, which propels water and propagules poleward, a flow intensifying due to climate change.Population genetic structure of the asterinid sea star Meridiastra calcar was investigated across its range in eastern Australia (12° of latitude, 2,500 km) from northern New South Wales to its poleward‐extending range in Tasmania at the southern edge influence of the East Australia Current.Population structure and connectivity of M. calcar were examined across six bioregions using six microsatellite loci (nuclear DNA) and the control region (mitochondrial DNA). The potential influence of the extent of M. calcar's intertidal rock platform habitat was also assessed.Genetic structure analysis indicated that the Hawkesbury Shelf contained distinct genetic clusters, whereas the two sites in the Batemans Shelf differed from each other, with Jervis Bay Marine Park having just one genetic cluster. The Manning Shelf, Twofold Shelf, and Bruny bioregions all had similar genetic composition.Strong self‐seeding (68–98%) was indicated by microsatellite loci for all bioregions, with lower (0.3–6.5%) migration between bioregions. Poleward (New South Wales to Tasmania) migration was low except from the Manning Shelf (30%).Conte...

Kole, TM, Pouwels, SD, Bults, R, Ketelaar, ME, Guryev, V, Koll, L, Kerstjens, HAM, Nawijn, MC, Faiz, A & van den Berge, M 2023, 'Airway wall splice quantitative trait locus analysis reveals novel downstream mechanisms for known asthma single-nucleotide polymorphisms', ERJ Open Research, vol. 9, no. 2, pp. 00413-2022.
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Kordzahiya, NE, Novikov, AA & Shiryaev, AN 2023, 'Kolmogorov's inequality for the maximum of the sum of random variables and its martingale analogues', Teoriya Veroyatnostei i ee Primeneniya, vol. 68, no. 3, pp. 565-585.
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Дается обзор результатов, связанных с распространением неравенства Колмогорова для распределения модуля максимума суммы центрированных независимых случайных величин на случай мартингалов, рассматриваемых в случайные моменты остановки.

Kordzakhia, NE, Novikov, AA & Shiryaev, AN 2023, 'The Kolmogorov Inequality for the Maximum of the Sum of Random Variables and Its Martingale Analogues', Theory of Probability & Its Applications, vol. 68, no. 3, pp. 457-472.
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Krishnan, S, DeMaere, MZ, Beck, D, Ostrowski, M, Seymour, JR & Darling, AE 2023, 'Rhometa: Population recombination rate estimation from metagenomic read datasets', PLOS Genetics, vol. 19, no. 3, pp. e1010683-e1010683.
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Prokaryotic evolution is influenced by the exchange of genetic information between species through a process referred to as recombination. The rate of recombination is a useful measure for the adaptive capacity of a prokaryotic population. We introduce Rhometa (https://github.com/sid-krish/Rhometa), a new software package to determine recombination rates from shotgun sequencing reads of metagenomes. It extends the composite likelihood approach for population recombination rate estimation and enables the analysis of modern short-read datasets. We evaluated Rhometa over a broad range of sequencing depths and complexities, using simulated and real experimental short-read data aligned to external reference genomes. Rhometa offers a comprehensive solution for determining population recombination rates from contemporary metagenomic read datasets. Rhometa extends the capabilities of conventional sequence-based composite likelihood population recombination rate estimators to include modern aligned metagenomic read datasets with diverse sequencing depths, thereby enabling the effective application of these techniques and their high accuracy rates to the field of metagenomics. Using simulated datasets, we show that our method performs well, with its accuracy improving with increasing numbers of genomes. Rhometa was validated on a real S. pneumoniae transformation experiment, where we show that it obtains plausible estimates of the rate of recombination. Finally, the program was also run on ocean surface water metagenomic datasets, through which we demonstrate that the program works on uncultured metagenomic datasets.

Kruk, D, Yeung, ACY, Faiz, A, ten Hacken, NHT, Timens, W, van Kuppevelt, TH, Daamen, W, Hof, D, Harmsen, MC, Rojas, M & Heijink, IH 2023, 'Gene expression profiles in mesenchymal stromal cells from bone marrow, adipose tissue and lung tissue of COPD patients and controls', Respiratory Research, vol. 24, no. 1, p. 22.
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Abstract Background Chronic obstructive pulmonary disease (COPD) is characterized by irreversible lung tissue damage. Novel regenerative strategies are urgently awaited. Cultured mesenchymal stem/stromal cells (MSCs) have shown promising results in experimental models of COPD, but differences between sources may impact on their potential use in therapeutic strategies in patients. Aim To assess the transcriptome of lung-derived MSCs (LMSCs), bone marrow-derived MSCs (BM-MSC) and adipose-derived MSCs (AD-MSCs) from COPD patients and non-COPD controls. Methods We studied differences in gene expression profiles between the MSC-subtypes, as well as between COPD and control using RNA sequencing (RNA-seq). Results We show that besides heterogeneity between donors, MSCs from different sources have strongly divergent gene signatures. The growth factors FGF10 and HGF were predominantly expressed in LMSCs. MSCs from all sources displayed altered expression profiles in COPD, with most pronounced significantly up- and downregulated genes in MSCs from adipose tissue. Pathway analysis revealed that the most differentially expressed genes in COPD-derived AD-MSCs are involved in extracellular matrix (ECM) binding and expression. In LMSCs, the gene that differed most strongly between COPD and control was CSGALNACT1, an ECM modulating gene. Conclusion Autologous ...

Kumar, NN, Chan, YL, Chen, H & Oliver, BG 2023, 'Editorial: Effects of environmental toxins on brain health and development', Frontiers in Molecular Neuroscience, vol. 16, p. 1149776.
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Kumar, R, Kumar, R, Sharma, N, Khurana, N, Singh, SK, Satija, S, Mehta, M & Vyas, M 2023, 'Corrigendum to “Pharmacological evaluation of bromelain in mouse model of Alzheimer’s disease” [NeuroToxicology 90 (2022) 19–34]', NeuroToxicology, vol. 99, pp. 332-332.
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Kumar, U, Rashmi, Srivastava, A, Kumari, N, Chatterjee, C & Raghuwanshi, NS 2023, 'Evaluation of Standardized MODIS-Terra Satellite-Derived Evapotranspiration Using Genetic Algorithm for Better Field Applicability in a Tropical River Basin', Journal of the Indian Society of Remote Sensing, vol. 51, no. 5, pp. 1001-1012.
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Kumari, V, Vishwas, S, Kumar, R, Kakoty, V, Khursheed, R, Babu, MR, Harish, V, Mittal, N, Singh, PK, Alharthi, NS, Hakami, MA, Aba Alkhayl, FF, Gupta, G, Rubis, GD, Paudel, KR, Singh, M, Zandi, M, Oliver, BG, Dua, K & Singh, SK 2023, 'An overview of biomedical applications for gold nanoparticles against lung cancer', Journal of Drug Delivery Science and Technology, vol. 86, pp. 104729-104729.
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Kumbhar, P, Kaur, J, De Rubis, G, Paudel, KR, Prasher, P, Patel, VK, Corrie, L, Chellappan, DK, Gupta, G, Singh, SK, Patravale, V, Disouza, J & Dua, K 2023, 'Inhalation drug delivery in combating pulmonary infections: Advances and challenges', Journal of Drug Delivery Science and Technology, vol. 89, pp. 105022-105022.
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L I, H, Huang, X, Cai, H, Herok, G, He, J, Su, Y, Li, W, Yi, C, Oliver, BG & Chen, H 2023, 'Mitochondrial dysfunction in a rat model and the related risk of metabolic disorders.', J Tradit Chin Med, vol. 43, no. 1, pp. 95-104.
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OBJECTIVE: To explore whether kidney deficiency (KYD) is prone to metabolic disorders may be linked to impaired mitochondrial function in thermogenesis and metabolic tissues. METHODS: A rat model of KYD was used, which was established using Sprague Dawley rat dams with warm preference subjected to herbal treatment that can improve kidney . The human relevance was confirmed by reduced serum corticosterone levels, and increased preference for warm location. RESULTS: KYD Rats were underdeveloped. Adenosine-triphosphate (ATP) production was reduced in the brown fat, but increased in the muscle. However, oxidative phosphorylated complexes to generate ATP and mitochondrial biogenesis marker were reduced in both tissues. When the second insult of high-fat diet (HFD) was introduced, KYD rats gained less weight yet developed more severe lipid and glucose metabolic disorders. This may be driven by disregulated liver gluconeogenesis marker forkhead box protein O1 and lipid metabolic regulator cholesterol 7 alpha-hydroxylase. CONCLUSION: KYD rats exhibited reduced mito-chondrial function in the brown fat, but were partially compensated by skeletal muscle, associated with the phenotype of warm preference and metabolic disorder, which was further exacerbated by additional HFD consumption. Future studies can focus on treatment targetting mitochondria function to reverse this phenotype.

Lai, CK, Merklein, M, Casas-Bedoya, A, Liu, Y, Madden, SJ, Poulton, CG, Steel, MJ & Eggleton, BJ 2023, 'Optimizing performance for an on-chip stimulated Brillouin scattering-based isolator', Journal of the Optical Society of America B, vol. 40, no. 3, pp. 523-523.
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Non-reciprocal optical components such as isolators and circulators are crucial for preventing catastrophic backreflection and controlling optical cross talk in photonic systems. While non-reciprocal devices based on Brillouin intermodal transitions have been experimentally demonstrated in chip-scale platforms, harnessing such interactions has required a suspended waveguide structure, which is challenging to fabricate and is potentially less robust than a non-suspended structure, thereby limiting the design flexibility. In this paper, we numerically investigate the performance of a Brillouin-based isolation scheme in which a dual-pump-driven optoacoustic interaction is used to excite confined acoustic waves in a traditional ridge waveguide. We find that acoustic confinement, and therefore the amount of Brillouin-driven mode conversion, can be enhanced by selecting an appropriate optical mode pair and waveguide geometry of two arsenic-based chalcogenide platforms. Further, we optimize the isolator design in its entirety, including the input couplers, mode filters, the Brillouin-active waveguide as well as the device fabrication tolerances. We predict such a device can achieve 30 dB isolation over a 38 nm bandwidth when 500 mW pump power is used; in the presence of a ± 10 n m fabrication-induced width error, such isolation can be maintained over a 5–10 nm bandwidth.

Lam, MMC, Koong, J, Holt, KE, Hall, RM & Hamidian, M 2023, 'Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins', Microbiology Spectrum, vol. 11, no. 1, p. e0247822.
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Though they contribute to the dissemination of genes that confer resistance to clinically important carbapenem and aminoglycoside antibiotics used to treat life-threatening Acinetobacter baumannii infections, plasmids found in Acinetobacter species have not been well studied. As these plasmids do not resemble those found in other Gram-negative pathogens, available typing systems are unsuitable.

Lankage, UM, Holt, SA, Bridge, S, Cornell, B & Cranfield, CG 2023, 'Triglyceride-Tethered Membrane Lipase Sensor', ACS Applied Materials & Interfaces.
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Sensors that can quickly measure the lipase activity from biological samples are useful in enzyme production and medical diagnostics. However, current lipase sensors have limitations such as requiring fluorescent labels, pH control of buffer vehicles, or lengthy assay preparation. We introduce a sparsely tethered triglyceride substrate anchored off of a gold electrode for the impedance sensing of real-time lipase activity. The tethered substrate is self-assembled using a rapid solvent exchange technique and can form an anchored bilayer 1 nm off the gold electrode. This allows for an aqueous reservoir region, providing access to ions transported through membrane defects caused by triglyceride enzymatic hydrolysis. Electrical impedance spectroscopy techniques can readily detect the decrease in resistance caused by enzymatically induced defects. This rapid and reliable lipase detection method can have potential applications in disease studies, monitoring of lipase production, and as point-of-care diagnostic devices.

Lapine, M & Gorlach, M 2023, 'Current trends and nonlinear effects in multilayered metamaterials—FF-1:IL01', Ceramics International, vol. 49, no. 14, pp. 24422-24427.
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Lau, V, Spindler, X & Roux, C 2023, 'The transfer of fibres between garments in a choreographed assault scenario', Forensic Science International, vol. 349, pp. 111746-111746.
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Our fundamental understanding of fibre transfer remains based on early seminal transfer studies that were largely mechanical simulations. However, transfer events in the real world are uncontrolled in nature. This study takes a novel approach to address this discrepancy, with skilled jiu-jitsu practitioners performing a choreographed 'standard' assault scenario to investigate the transfer of fibres between a cotton T-shirt and cotton/polyester hoody. Garments were collected immediately after the scenario and examined for the number, length and zonal distribution of transferred fibres. It was observed that cotton transferred the most fibres, on average twice as many from blended hoodies than T-shirts; whilst polyester transferred the least. Shorter fibres transferred and were recovered more readily than longer fibres; however, it was more likely to recover polyester fibres> 5 mm. The number and length of fibres transferred from the attacker's garment mainly depended on the construction of the donor textile (including sheddability) and properties of the fibres. Conversely, properties of the recipient textile were more significant factors when considering transfer from the victim's garment. Location of recovered fibres was found to be dependent on the wearer's role, but generally, upper zones and sleeves of both garments were most populated. Overall, these results will contribute to grow our current knowledge base regarding fibre transfer between donor and recipient textiles in a common assault situation. This will ultimately aid experts support evaluation with regards to competing hypotheses such as in a Bayesian framework.

Le Brun, AP, Huang, T-Y, Pullen, S, Nelson, ARJ, Spedding, J & Holt, SA 2023, 'Spatz: the time-of-flight neutron reflectometer with vertical sample geometry at the OPAL research reactor', Journal of Applied Crystallography, vol. 56, no. 1, pp. 18-25.
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The Spatz neutron beam instrument is the second time-of-flight neutron reflectometer to be installed at the OPAL research reactor. The instrument was formerly the V18 BioRef reflectometer at the BER-II reactor in Berlin and was transferred to Australia in 2016. Subsequently the instrument was re-installed in the neutron guide hall of the OPAL reactor at the end position of the CG2B cold-neutron guide and recommissioned. The instrument performance has not been compromised by the move, with reflectivity achieved down to 10−7 and good counting statistics within a reasonable time frame using a wavelength range of 2–20 Å. Several different samples at the solid–air interface and the solid–liquid interface have been measured to demonstrate the instrument's capabilities.

Le Reun, N, Bramucci, A, Ajani, P, Khalil, A, Raina, J-B & Seymour, JR 2023, 'Temporal variability in the growth-enhancing effects of different bacteria within the microbiome of the diatom Actinocyclus sp.', Frontiers in Microbiology, vol. 14, p. 1230349.
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Reciprocal metabolite exchanges between diatoms and bacteria can enhance the growth of both partners and therefore fundamentally influence aquatic ecosystem productivity. Here, we examined the growth-promoting capabilities of 15 different bacterial isolates from the bacterial community associated with the marine diatom Actinocyclus sp. and investigated the magnitude and timing of their effect on the growth of this diatom. In the presence of its microbiome, Actinocyclus sp. growth was significantly enhanced relative to axenic cultures. Co-culture with each of the 15 bacterial isolates examined here (seven Rhodobacteraceae, four Vibrionaceae, two Pseudoalteromonadaceae, one Oceanospirillaceae and one Alteromonadaceae) increased the growth of the diatom host, with four isolates inducing rates of growth that were similar to those delivered by the diatom’s full microbiome. However, the timing and duration of this effect differed between the different bacteria tested. Indeed, one Rhodobacteraceae and one Alteromonadaceae enhanced Actinocyclus sp. cell numbers between days 0–6 after co-incubation, five other Rhodobacteraceae promoted diatom cell numbers the most between days 8–12, whilst four Vibrionaceae, one Oceanospirillaceae and one Rhodobacteraceae enhanced Actinocyclus sp. cell abundance between days 14–16. These results are indicative of a succession of the growth-enhancing effects delivered by diverse bacteria throughout the Actinocyclus sp. life cycle, which will likely deliver sustained growth benefits to the diatom when its full microbiome is present.

Lei, X, Ma, Z, Bai, L, Wang, L, Ding, Y, Song, S, Song, A, Dong, H, Tian, H, Tian, H, Meng, X, Liu, H, Sun, B, Shao, G & Wang, G 2023, 'Porous ZnP matrix for long‐lifespan and dendrite‐free Zn metal anodes', Battery Energy, vol. 2, no. 6.
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AbstractThe reversibility of Zn plating/stripping during cycling is adversely affected by dendritic growth, electrochemical corrosion, surface passivation, and hydrogen generation on the Zn anodes for rechargeable aqueous zinc ion batteries (ZIBs). Herein, through an ordinary anodic etching process, a uniform porous ZnP matrix protective layer was created on the Zn foil (Zn@ZnP). The large and accessible specific surface area of the prepared Zn@ZnP can facilitate contact with the electrolyte, accelerating the migration and enhancing the desolvation of Zn2+, effectively enhancing the Zn deposition kinetics. According to studies from scanning electron microscopy (SEM) and multiscale optical microscopy, the Zn@ZnP electrode effectively inhibits the growth of dendrites with excellent Zn plating/stripping reversibility. In consequence, the symmetric cell with the Zn@ZnP electrodes displays a long‐term cycle life of over 1260 h at 10  mA  cm−2. The full cell, consisting of Zn@ZnP anodes and MnO2‐based cathode, demonstrated a high discharge capacity of 145 mAh g−1 after cycling 500 times at the current density of 1000 mA  g−1. A scalable method for designing a homogeneous anode protection layer enables dendrite‐free zinc metal anodes, paving the way for interface modification of other metal anodes.

Letnic, M, Roberts, B, Hodgson, M, Ross, AK, Cuartas, S, Lapwong, Y, Price, O, Sentinella, N & Webb, JK 2023, 'Fire severity influences the post‐fire habitat structure and abundance of a cool climate lizard', Austral Ecology, vol. 48, no. 7, pp. 1440-1453.
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AbstractIn the spring and summer of 2019–2020, the ‘Black Summer’ bushfires burned more than 97 000 km2 of predominantly Eucalyptus dominated forest habitat in eastern Australia. The Black Summer bushfires prompted great concern that many species had been imperilled by the fires. Here, we investigate the effects that fire severity had on the habitat and abundance of a cool climate lizard Eulamprus tympanum that was identified as a species of concern because 37% of its habitat was burnt in the Black Summer bushfires. We quantified habitat structure and the abundance of E. tympanum at sites which were unburnt, burnt at low severity and at high severity 10, 15 and 23 months after the fires. Our classification of fire severity based on scorch height and canopy status corresponded well with the Australian Government Google Earth Engine Burnt Area Map (AUS GEEBAM) fire severity layer. Ten months after the fires, sites burnt at high severity had less canopy cover, more bare ground and less fine fuel than sites burnt at low severity or unburnt sites. The abundance of E. tympanum varied with survey occasion and was greatest during the warmest sampling period and lowest during the coolest sampling period. The abundance of E. tympanum was consistently lower on sites burnt at high severity than sites burnt at low severity or unburnt sites. Our findings show that higher severity fires had a greater effect on E. tympanum than low severity fires. Our results suggest that E. tympanum were likely to have persisted in burnt sites, with populations in low severity and unburnt sites facilitating population recovery in areas burnt at high severity. Our results also suggest that wildfire impacts on E. tympanum...

Lev, B, Chennath, M, Cranfield, CG, Cornelius, F, Allen, TW & Clarke, RJ 2023, 'Involvement of the alpha-subunit N-terminus in the mechanism of the Na+,K+-ATPase', Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol. 1870, no. 7, pp. 119539-119539.
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Li, C, Tareen, AK, Khan, K, Long, J, Hussain, I, Khan, MF, Iqbal, M, Xie, Z, Zhang, Y, Mahmood, A, Mahmood, N, Ahmad, W & Zhang, H 2023, 'Highly efficient, remarkable sensor activity and energy storage properties of MXenes and borophene nanomaterials', Progress in Solid State Chemistry, vol. 70, pp. 100392-100392.
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Li, D, Elankumaran, P, Kudinha, T, Kidsley, AK, Trott, DJ, Jarocki, VM & Djordjevic, SP 2023, 'Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids', Microbial Genomics, vol. 9, no. 7.
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Extraintestinal pathogenic Escherichia coli (ExPEC) are the most frequent cause of urinary tract infections (UTIs) globally. Most studies of clinical E. coli isolates are selected based on their antimicrobial resistance (AMR) phenotypes; however, this selection bias may not provide an accurate portrayal of which sequence types (STs) cause the most disease. Here, whole genome sequencing (WGS) was performed on 320 E. coli isolates from urine samples sourced from a regional hospital in Australia in 2006. Most isolates (91%) were sourced from patients with UTIs and were not selected based on any AMR phenotypes. No significant differences were observed in AMR and virulence genes profiles across age sex, and uro-clinical syndromes. While 88 STs were identified, ST73, ST95, ST127 and ST131 dominated. F virulence plasmids carrying senB-cjrABC (126/231; 55%) virulence genes were a feature of this collection. These senB-cjrA...

Li, L, Cao, X, Huo, J, Qu, J, Chen, W, Liu, C, Zhao, Y, Liu, H & Wang, G 2023, 'High valence metals engineering strategies of Fe/Co/Ni-based catalysts for boosted OER electrocatalysis', Journal of Energy Chemistry, vol. 76, pp. 195-213.
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Li, L, Short, FL, Hassan, KA, Naidu, V, Pokhrel, A, Nagy, SS, Prity, FT, Shah, BS, Afrin, N, Baker, S, Parkhill, J, Cain, AK & Paulsen, IT 2023, 'Systematic analyses identify modes of action of ten clinically relevant biocides and antibiotic antagonism in Acinetobacter baumannii', NATURE MICROBIOLOGY, vol. 8, no. 11, pp. 1995-+.
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Li, Q, Han, N, Chai, J, Zhang, W, Du, J, Tian, H, Liu, H, Wang, G & Tang, B 2023, 'Strategies to improve metal-organic frameworks and their derived oxides as lithium storage anode materials', Energy, vol. 282, pp. 128378-128378.
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Li, Y, Faiz, A, Moshage, H, Schilling, L & Kamps, JAAM 2023, 'Responses of retinal and brain microvasculature to streptozotocin induced diabetes revealed by global expression profiling', Diabetes and Vascular Disease Research, vol. 20, no. 1, pp. 147916412211475-147916412211475.
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This study aims to determine the effects of diabetes in the retinal and brain microvasculature through gene expression profiling. Twelve male Wistar rats were randomly divided into two groups: streptozotocin-induced diabetic rats and time-matched nondiabetic rats. The retinal microvessels (RMVs) and brain microvessels (BMVs) were mechanically isolated from individual rats. Differentially expressed genes (DEGs) in diabetic and nondiabetic microvessels were identified by cDNA microarrays analysis. In RMVs, we identified 43 DEGs, of which 20 were upregulated while 23 were downregulated by diabetes. In BMVs, 35 genes DEGs were identified, of which 22 were upregulated and 13 were downregulated by diabetes. Altered expression of the Nars, Gars, Mars, Iars, Yars, Bcl2, Nqo1, NR4A3, Gpd1, Stc1, Tsc22d3, Tnfrsf21 mRNA as observed in the microarray analyses, was confirmed by quantitative RT-PCR. The aminoacyl-tRNA synthetases (aaRSs) pathway in RMVs was significantly overrepresented as compared to BMVs. Our study demonstrates for the first time that in the brain microvasculature multiple compensatory mechanisms exists, serving to protect brain tissue from diabetic insults, whereas these mechanisms are not activated in the retinal microvasculature. This provides new insights as to why brain microvasculature is less susceptible to diabetes.

Liau, S, Wang, JZ, Zagarella, E, Paulus, P, Dang, NHQH, Rawling, T, Murray, M & Zhou, F 2023, 'An update on inflammation in uveal melanoma', Biochimie, vol. 212, pp. 114-122.
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Lin, G, Khan, JU, Zhand, S, Liu, Y & Jin, D 2023, 'Modular DNAzymes-Hydrogel Membrane Carriers for Highly Sensitive Isothermal Cross-Cascade Detection of Pathogenic Bacteria Nucleic Acids', Analytical Chemistry, vol. 95, no. 35, pp. 13353-13360.
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The increasing prevalence of antimicrobial resistance has called for improved diagnostic testing of pathogenic bacteria. However, the development of rapid, cost-effective, and easy-to-use tests for bacterial infections remains a constant challenge. Here, we report a class of modular hydrogel membrane carriers incorporated with composite DNAzymes, which enable rapid and highly sensitive detection of pathogenic bacteria gene target analytes. We apply free radical polymerization to incorporate composite DNAzymes, consisting of an RNA substrate component and a DNAzyme component (e.g., 10-23 or 8-17 DNAzymes), into polyethylene glycol diacrylate polymer networks. Initiated by a nucleic acid target acting as an assembly facilitator, multicomponent DNAzymes are combined to cleave the RNA substrate component in the hydrogel carriers, which releases the DNAzyme component to cleave RNA reporter probes to generate fluorescence. We modulate the morphology, composition, and microporous structures of the DNAzyme carriers to achieve quantitative assay performance. We demonstrate a rapid and high-sensitivity detection of C. trachomatis gene target analytes as low as 50 fM in a short assay time of 25 min. The work represents a crucial step forward in the development of a generic, isothermal, and protein enzyme-free pathogenic bacteria testing platform technology.

Lin, J, Xing, B & Jin, D 2023, 'Optical Bioimaging and Therapy', Advanced Optical Materials, vol. 11, no. 11.
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Liu, L, Liu, Y, Zhang, X, Yuan, YL, Chen, ZH, Chen-Yu Hsu, A, Oliver, BG, Xie, M, Qin, L, Li, WM, Liu, D, Wang, G & Wood, LG 2023, 'Dyslipidemia Is Associated With Worse Asthma Clinical Outcomes: A Prospective Cohort Study', The Journal of Allergy and Clinical Immunology: In Practice, vol. 11, no. 3, pp. 863-872.e8.
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Liu, Y, Lin, G, Medina-Sánchez, M, Guix, M, Makarov, D & Jin, D 2023, 'Responsive Magnetic Nanocomposites for Intelligent Shape-Morphing Microrobots', ACS Nano, vol. 17, no. 10, pp. 8899-8917.
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Liu, Y, Wen, S, Wang, F, Zuo, C, Chen, C, Zhou, J & Jin, D 2023, 'Population Control of Upconversion Energy Transfer for Stimulation Emission Depletion Nanoscopy', Advanced Science, vol. 10, no. 20.
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AbstractUpconverting stimulated emission depletion microscopy (U‐STED) is emerging as an effective approach for super‐resolution imaging due to its significantly low depletion power and its ability to surpass the limitations of the square‐root law and achieve higher resolution. Though the compelling performance, a trade‐off between the spatial resolution and imaging quality in U‐STED has been recognized in restricting the usability due to the low excitation power drove high depletion efficiency. Moreover, it is a burden to search for the right power relying on trial and error as the underpinning mechanism is unknown. Here, a method is proposed that can easily predict the ideal excitation power for high depletion efficiency with the assistance of the non‐saturate excitation based on the dynamic cross‐relaxation (CR) energy transfer of upconversion nanoparticles. This allows the authors to employ the rate equation model to simulate the populations of each relevant energy state of lanthanides and predict the ideal excitation power for high depletion efficiency. The authors demonstrate that the resolution of STED with the assistance of nonsaturated confocal super‐resolution results can easily achieve the highest resolution of sub‐40 nm, 1/24th of the excitation wavelengths. The finding on the CR effect provides opportunities for population control in realizing low‐power high‐resolution nanoscopy.

Liu, Y, Zhou, J, Wen, S, Wang, F, Wu, H, Chen, Q, Zuo, C & Jin, D 2023, 'On-Chip Mirror Enhanced Multiphoton Upconversion Super-Resolution Microscopy', Nano Letters, vol. 23, no. 12, pp. 5514-5519.
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Lockwood, TE, Banati, RB, Nikagolla, C, Violi, JP & Bishop, DP 2023, 'Concentration and Distribution of Toxic and Essential Elements in Traditional Rice Varieties of Sri Lanka Grown on an Anuradhapura District Farm', Biological Trace Element Research.
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AbstractToxic heavy metals have been the focus of many investigations into chronic kidney disease of unknown aetiology (CKDu) within Sri Lanka. It has been hypothesised that exposure to nephrotoxic arsenic, cadmium and lead could play a role in the development of CKDu, and these metals have previously been found in unsafe concentrations in Sri Lankan rice. Traditional varieties of Sri Lankan rice remain popular due to their perceived health benefits, but their uptake of trace and toxic heavy metals remained unexplored. Here, we report a one-time, cross-sectional dataset on the concentrations of essential and toxic elements present in eleven samples of polished and unpolished traditional rice varieties, all regularly grown and sold in the Anuradhapura district, a CKDu hotspot. All rice was sourced from the same farm, with the exception of one store bought sample grown on another, unidentified farm. Cadmium concentrations varied significantly between varieties, and potentially unsafe concentrations of cadmium were detected in the store-bought sample (Suwadel, 113±13 μg kg−1). Elemental imaging of the grains revealed lead to be stored mainly in the rice bran, which is removed during polishing, while cadmium was distributed in the edible portion of the grain. Essential elements were generally higher in the traditional rice varieties than those reported for non-traditional varieties and are a potential source of trace elements for nutrient-deficient communities. The concentration of selenium, an element that plays a protective role in the kidneys, was too low to provide the minimum recommended intake. The methods developed in this study could be applied to a more comprehensive study of elemental uptake of rice under controlled growing conditions.

Loo, S, Roberts, AW, Anstee, NS, Kennedy, GA, He, S, Schwarer, AP, Enjeti, AK, D’Rozario, J, Marlton, P, Bilmon, IA, Taper, J, Cull, G, Tiley, C, Verner, E, Hahn, U, Hiwase, DK, Iland, HJ, Murphy, N, Ramanathan, S, Reynolds, J, Ong, DM, Tiong, IS, Wall, M, Murray, M, Rawling, T, Leadbetter, J, Rowley, L, Latimer, M, Yuen, S, Ting, SB, Fong, CY, Morris, K, Bajel, A, Seymour, JF, Levis, MJ & Wei, AH 2023, 'Sorafenib plus intensive chemotherapy in newly diagnosed FLT3-ITD AML: a randomized, placebo-controlled study by the ALLG', Blood, vol. 142, no. 23, pp. 1960-1971.
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Abstract Sorafenib maintenance improves outcomes after hematopoietic cell transplant (HCT) for patients with FMS-like tyrosine kinase 3–internal tandem duplication (FLT3-ITD) acute myeloid leukemia (AML). Although promising outcomes have been reported for sorafenib plus intensive chemotherapy, randomized data are limited. This placebo-controlled, phase 2 study (ACTRN12611001112954) randomized 102 patients (aged 18-65 years) 2:1 to sorafenib vs placebo (days 4-10) combined with intensive induction: idarubicin 12 mg/m2 on days 1 to 3 plus either cytarabine 1.5 g/m2 twice daily on days 1, 3, 5, and 7 (18-55 years) or 100 mg/m2 on days 1 to 7 (56-65 years), followed by consolidation and maintenance therapy for 12 months (post-HCT excluded) in newly diagnosed patients with FLT3-ITD AML. Four patients were excluded in a modified intention-to-treat final analysis (3 not commencing therapy and 1 was FLT3-ITD negative). Rates of complete remission (CR)/CR with incomplete hematologic recovery were high in both arms (sorafenib, 78%/9%; placebo, 70%/24%). With 49.1-months median follow-up, the primary end point of event-free survival (EFS) was not improved by sorafenib (2-year EFS 47.9% vs 45.4%; hazard ratio [HR], 0.87; 95% confidence interval [CI], 0.51-1.51; P = .61). Two-year overall survival (OS) was 67% in the sorafenib arm and 58% in the placebo arm (HR, 0.76; 95% CI, 0.42-1.39). For patients who received HCT in first remission, the 2-year OS rates were 84% and 67% in the sorafenib and placebo arms, respectively (HR, 0.45; 95% CI, 0.18-1.12; P = .08). In exploratory analyses, FLT3-ITD measurable residual disease (MRD) negative status (&lt;0.001%) after induction was associated with improved 2-year OS (83% vs 60%; HR, 0.4; 95% CI, 0.17-0.93; P = .028). In conclusion, routine use of pretransplant sorafenib plus chemotherapy in unselected patients with FLT3-ITD AML is not supported by this study.

Lotfi, M, Tambuwala, MM, Shahcheraghi, SH, Ayatollahi, J, Aljabali, AAA, Al-Zoubi, MS, Panda, PK, Mishra, V, Satija, S, Charbe, NB, Serrano-Aroca, Á, Bahar, B, Takayama, K, Goyal, R, Bhatia, A, Almutary, AG, Alnuqaydan, AM, Mishra, Y, Negi, P, Courtney, A, McCarron, PA & Bakshi, HA 2023, 'Gene Therapy for Neuropsychiatric Disorders: Potential Targets and Tools', CNS & Neurological Disorders - Drug Targets, vol. 22, no. 1, pp. 51-65.
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Abstract:Neuropsychiatric disorders that affect the central nervous system cause considerable pressures on the health care system and have a substantial economic burden on modern societies. The present treatments based on available drugs are mostly ineffective and often costly. The molecular process of neuropsychiatric disorders is closely connected to modifying the genetic structures inherited or caused by damage, toxic chemicals, and some current diseases. Gene therapy is presently an experimental concept for neurological disorders. Clinical applications endeavor to alleviate the symptoms, reduce disease progression, and repair defective genes. Implementing gene therapy in inherited and acquired neurological illnesses entails the integration of several scientific disciplines, including virology, neurology, neurosurgery, molecular genetics, and immunology. Genetic manipulation has the power to minimize or cure illness by inducing genetic alterations at endogenous loci. Gene therapy that involves treating the disease by deleting, silencing, or editing defective genes and delivering genetic material to produce therapeutic molecules has excellent potential as a novel approach for treating neuropsychiatric disorders. With the recent advances in gene selection and vector design quality in targeted treatments, gene therapy could be an effective approach. This review article will investigate and report the newest and the most critical molecules and factors in neuropsychiatric disorder gene therapy. Different genome editing techniques available will be evaluated, and the review will highlight preclinical research of genome editing for neuropsychiatric disorders while also evaluating current limitations and potential strategies to overcome genome editing advancements.

Lubchenco, J, Camp, EF, Vargas, CA, Belhabib, D, Anna, Z, Amon, DJ, Metaxas, A & Harden-Davies, H 2023, 'Priorities for progress towards Sustainable Development Goal 14 ‘Life below water’', Nature Ecology & Evolution, vol. 7, no. 10, pp. 1564-1569.
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Luo, X, Zhang, C, Yu, Z, Wen, S & Xian, Y 2023, 'Recent advances in responsive lanthanide-doped luminescence nanoprobes in the near-infrared-II window', TrAC Trends in Analytical Chemistry, vol. 169, pp. 117368-117368.
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Luo, Y, Liu, Q, He, P, Li, L, Zhang, Z, Li, X, Bao, G, Wong, K, Tanner, PA & Jiang, L 2023, 'Responsive Regulation of Energy Transfer in Lanthanide‐Doped Nanomaterials Dispersed in Chiral Nematic Structure', Advanced Science, vol. 10, no. 27.
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AbstractThe responsive control of energy transfer (ET) plays a key role in the broad applications of lanthanide‐doped nanomaterials. Photonic crystals (PCs) are excellent materials for ET regulation. Among the numerous materials that can be used to fabricate PCs, chiral nematic liquid crystals are highly attractive due to their good photoelectric responsiveness and biocompatibility. Here, the mechanisms of ET and the photonic effect of chiral nematic structures on ET are introduced; the regulation methods of chiral nematic structures and the resulting changes in ET of lanthanide‐doped nanomaterials are highlighted; and the challenges and promising opportunities for ET in chiral nematic structures are discussed.

Luu, LDW, Kasimov, V, Phillips, S, Myers, GSA & Jelocnik, M 2023, 'Genome organization and genomics in Chlamydia: whole genome sequencing increases understanding of chlamydial virulence, evolution, and phylogeny', Frontiers in Cellular and Infection Microbiology, vol. 13, p. 1178736.
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The genus Chlamydia contains important obligate intracellular bacterial pathogens to humans and animals, including C. trachomatis and C. pneumoniae. Since 1998, when the first Chlamydia genome was published, our understanding of how these microbes interact, evolved and adapted to different intracellular host environments has been transformed due to the expansion of chlamydial genomes. This review explores the current state of knowledge in Chlamydia genomics and how whole genome sequencing has revolutionised our understanding of Chlamydia virulence, evolution, and phylogeny over the past two and a half decades. This review will also highlight developments in multi-omics and other approaches that have complemented whole genome sequencing to advance knowledge of Chlamydia pathogenesis and future directions for chlamydial genomics.

Ma, H, Hu, M, Zhang, C, Jia, J, Fu, S, Wei, Z & Yun, K 2023, 'HPLC-MS/MS determination and the postmortem distribution or postmortem redistribution of paraquat and its metabolites in four fatal intoxication cases', Forensic Science International, vol. 345, pp. 111606-111606.
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Ma, H, Yu, K, Wang, H, Liu, J, Cheng, YY, Kang, Y, Wang, H, Zhang, J & Song, K 2023, 'Fabrication and detection of a novel hybrid conductive scaffold based on alginate/gelatin/carboxylated carbon nanotubes (Alg/Gel/mMWCNTs) for neural tissue engineering', Tissue and Cell, vol. 80, pp. 101995-101995.
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Ma, H, Zheng, L, Yang, S, Cheng, YY, Liu, T, Wu, S, Wang, H, Zhang, J & Song, K 2023, 'Construction and properties detection of 3D micro-structure scaffolds base on decellularized sheep kidney before and after crosslinking', Journal of Biomaterials Applications, vol. 37, no. 9, pp. 1593-1604.
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Decellularized extracellular matrix is one form of natural material in tissue engineering. The process of dECM retains the tissue microstructure, provides good cell adhesion sites, maintains most of biological signals that promotes the survival and differentiation ability of cells. In this study, sheep kidney was decellularized followed by histochemical staining, elemental analysis and scanning electron microscopy characterizations. The dECM scaffold was prepared with different sequences of freeze drying technology, crosslinking and the water absorption, porosity, mechanical strength with subsequent thermogravimetric analysis, Infrared spectroscopy and biocompatibility tests. Our results indicated that these decellularized treatments of sheep kidney can effectively remove DNA and retain uniform pore size distribution. After crosslinking the scaffold’s water absorption decreased from 987.56 ± 40.21% to 934.39 ± 39.61%, the porosity decreased from 89.64 ± 3.2% to 85.09 ± 17.63%, and the compression modulus increased from 304.32 ± 25.43 kPa to 459.53 ± 38.92 kPa, with thermal process the percentage of weight loss decreased from 66.57% to 44.731%, in addition, the composition didn’t change significantly, crosslinking could also promote the stability. In terms of biocompatibility, the number of viable cells increased significantly with the days. In conclusion, the crosslinked decellularized sheep kidney extracellular matrix scaffold reduced water absorption and porosity slightly, but has a significant increase in mechanical properties, and presented excellent biocompatibility which are beneficial to cell adhesion, growth and differentiation.

Ma, Z, Song, A, Liu, Z, Guo, Y, Yang, X, Li, Q, Fan, Y, Dai, L, Tian, H, Qin, X, Liu, H, Shao, G & Wang, G 2023, 'Nanoconfined Expansion Behavior of Hollow MnS@Carbon Anode with Extended Lithiation Cyclic Stability', Advanced Functional Materials, vol. 33, no. 28.
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AbstractThe construction of hollow nanostructure by compositing with carbonaceous materials is generally considered an effective strategy to mitigate the drastic volume expansion of transition metal sulfides (TMSs) with high theoretical specific capacity in the process of lithium storage. However, designing well‐controlled architectures with extended lithiation cyclic stability, and ease the expansion of the electroactive materials into the reserved hollow spaces still needs to be developed. Herein, using MnS as an example, the hollow double‐shell carbon‐coated TMSs architecture is designed to achieve the controllable operation of shell thickness to regulate interfacial stress. The functional architecture enables the high‐capacity MnS to reach reversible capacities and extended lithiation cycling stability at high current densities. In situ transmission electron microscopy, optical observation characterizations and finite elements are used to analyze the nanoconfined expansion behavior of hollow MnS@C anodes. The as‐designed hollow structure with a carbon shell thickness ≈12.5 nm can effectively restrict the drastic expansion of MnS nanoshell into inner voids with compressive stress. This study demonstrates a general strategy to design functional carbon coating metal sulfides with tailored interfacial stress.

MacDermott-Opeskin, H, Clarke, C, Wu, X, Roseblade, A, York, E, Pacchini, E, Roy, R, Cranfield, C, Gale, PA, O'Mara, ML, Murray, M & Rawling, T 2023, 'Protonophoric and mitochondrial uncoupling activity of aryl-carbamate substituted fatty acids', Organic & Biomolecular Chemistry, vol. 21, no. 1, pp. 132-139.
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Aryl-carbamate substituted fatty acids are protonophores that uncouple mitochondrial oxidative phosphorylation. The proton transport cycle requires self-assembly into membrane permeable dimers. The findings demonstrate the anion transport capability of the carbamate group.

Macdonald Miller, S, Herdean, A, Gupta, V, Signal, B, Abbriano, RM, Ralph, PJ & Pernice, M 2023, 'Differential gene expression in a subpopulation of Phaeodactylum tricornutum with enhanced growth and carotenoid production after FACS-mediated selection', Journal of Applied Phycology, vol. 35, no. 6, pp. 2777-2787.
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AbstractFluorescence-Activated Cell Sorting (FACS) is a powerful method with many applications in microalgal research, especially for screening and selection of cells with improved phenotypes. However, the technology requires review of gene expression changes responsible for enhanced phenotypes in sorted populations. Phaeodactylum tricornutum cells were sorted using FACS with excitation/emission parameters targeted to favouring the industrially-relevant carotenoid fucoxanthin. The resulting cultures showed significantly higher growth rate (1.10 ×), biomass (1.30 ×), chlorophyll a levels (1.22 ×) and fucoxanthin content (1.28 ×) relative to the wild-type strain. RNA-seq was used to elucidate the underlying molecular-level regulatory changes associated with these traits and represents the first study do so on FACS-sorted microalgal cultures. Transcriptome analysis corroborated evidence of increased chlorophyll a and fucoxanthin, showing enrichment for the genes/pathways for tetrapyrrole biosynthesis and for suites of genes directly related to photosynthesis. Only three genes were upregulated in the MEP (non-mevalonate) pathway to carotenoid biosynthesis pathway, suggesting either a strong influence of IDI, CRTISO5 and ZEP1 on fucoxanthin biosynthesis or a post-transcriptional or post-translational mechanism for the observed increase in fucoxanthin content.

Machungo, CW, Berna, AZ, McNevin, D, Wang, R, Harvey, J & Trowell, S 2023, 'Evaluation of performance of metal oxide electronic nose for detection of aflatoxin in artificially and naturally contaminated maize', Sensors and Actuators B: Chemical, vol. 381, pp. 133446-133446.
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Madin, JS, McWilliam, M, Quigley, K, Bay, LK, Bellwood, D, Doropoulos, C, Fernandes, L, Harrison, P, Hoey, AS, Mumby, PJ, Ortiz, JC, Richards, ZT, Riginos, C, Schiettekatte, NMD, Suggett, DJ & van Oppen, MJH 2023, 'Selecting coral species for reef restoration', Journal of Applied Ecology, vol. 60, no. 8, pp. 1537-1544.
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AbstractHumans have long sought to restore species but little attention has been directed at how to best select a subset of foundation species for maintaining rich assemblages that support ecosystems, like coral reefs and rainforests, which are increasingly threatened by environmental change.We propose a two‐part hedging approach that selects optimized sets of species for restoration. The first part acknowledges that biodiversity supports ecosystem functions and services, and so it ensures precaution against loss by allocating an even spread of phenotypic traits. The second part maximizes species and ecosystem persistence by weighting species based on characteristics that are known to improve ecological persistence—for example abundance, species range and tolerance to environmental change.Using existing phenotypic‐trait and ecological data for reef building corals, we identified sets of ecologically persistent species by examining marginal returns in occupancy of phenotypic trait space. We compared optimal sets of species with those from the world's southern‐most coral reef, which naturally harbours low coral diversity, to show these occupy much of the trait space. Comparison with an existing coral restoration program indicated that current corals used for restoration only cover part of the desired trait space and programs may be improved by including species with different traits.Synthesis and applications. While there are many possible criteria for selecting species for restoration, the approach proposed here addresses the need to insure against unpredictable losses of ecosystem services by focusing on a wide range of phenotypic traits and ecological characteristics. Furthermore, the flexibility of the...

Mahant, S, Sharma, AK, Gandhi, H, Wadhwa, R, Dua, K & Kapoor, DN 2023, 'Emerging Trends and Potential Prospects in Vaginal Drug Delivery', Current Drug Delivery, vol. 20, no. 6, pp. 730-751.
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Abstract:The vagina is an essential part of the female reproductive system and offers many potentialbenefits over conventional drug delivery, including a large surface area for drug absorption, relativelylow enzymatic activity, avoiding first-pass effects, and ease of administration. The vaginalmucosal cavity is an effective route for administering therapeutic agents that are intended both forlocal and systemic administration. The present review provides a comprehensive overview of recenttrends and developments in vaginal drug delivery. Marketed formulations and products under clinicalstudy are also reviewed. Various novel vaginal delivery systems have been studied in recentyears as effective tools for delivering a range of therapeutic agents to the vagina. These systems offernumerous benefits, including sustained delivery, improved bioavailability, effective permeation,and higher efficacy. The recent focus of the scientific community is on the development of safe andefficient drug delivery systems, such as nanoparticles, microparticles, vesicular systems, vaginalrings, microneedles, etc., for vaginal application. Various factors, such as the physicochemical propertiesof the drugs, the volume and composition of the vaginal fluid, the pH of the vaginal fluid, thethickness of the vaginal epithelium, and the influence of sexual intercourse may influence the releaseof drugs from the delivery system and subsequent absorption from the vaginal route. To date,only a limited number of in vivo studies on novel vaginal DDS have been reported. Additionally,drug release kinetics under varying vaginal environments is also not well understood. More researchis needed to ensure the suitability, biocompatibility, and therapeutic effectiveness of novel DDS forvaginal delivery. Although numerous strategies and interventions have been developed, clinicaltranslation of these systems remains a challenge. The toxi...

Mahmutoglu, G, Topsakal, A, Altan, E, Kuskonmaz, N, Daglilar, S, Oktar, FN, Erdemir, G, Kuruca, SE, Akyol, S, Gunduz, O & Ben-Nissan, B 2023, 'Effects of temperature and pH on the synthesis of nanohydroxyapatite powders by chemical precipitation', Journal of the Australian Ceramic Society, vol. 59, no. 5, pp. 1433-1441.
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Malik, R, Paudel, KR, Manandhar, B, De Rubis, G, Shen, J, Mujwar, S, Singh, TG, Singh, SK, Gupta, G, Adams, J, MacLoughlin, R, Oliver, BGG, Hansbro, PM, Chellappan, DK & Dua, K 2023, 'Agarwood oil nanoemulsion counteracts LPS-induced inflammation and oxidative stress in RAW264.7 mouse macrophages', Pathology - Research and Practice, vol. 251, pp. 154895-154895.
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Mallen‐Cooper, M, Cornwell, WK, Slavich, E, Sabot, MEB, Xirocostas, ZA & Eldridge, DJ 2023, 'Limited range shifting in biocrusts despite climate warming: A 25‐year resurvey', Journal of Ecology, vol. 111, no. 10, pp. 2194-2207.
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AbstractThe ranges of many species globally have already shifted to maintain climatic equilibrium in the face of climate change.Biocrusts—soil surface dwelling communities of lichens, bryophytes and microbes—play important functional roles in many ecosystems, particularly in drylands. Compared to better studied animal and plant taxa, dryland biocrusts have different establishment requirements and have never been assessed for historical range shifts.Here, we revisited the sites (N = 204) of a 25‐year‐old biocrust survey across a large area (400,000 km2) of drylands in south‐eastern Australia. We used quadratic models to quantify changes in the climate niches of 15 lichen, eight moss and five liverwort taxa, as well as biocrust cover and richness.Our models showed that the observed climatic niches of most taxa have become hotter and drier in the past quarter century, yet the responses of the vast majority of taxa are consistent with remaining in the same geographic space. A similar pattern was observed at the community level, where the peak of biocrust cover and richness now occurs in a hotter, drier environment. Notable exceptions were the liverwort Riccia lamellosa and lichens in the genera Cladonia and Xanthoparmelia, which showed signs of contraction at their arid range edges.Unlike more mobile taxa, most biocrust species have yet to shift geographically and may already be lagging behind the pace of climate change. One explanation for the mortality lag is that long‐term climate variability in the system is extensive, which may have selected for the ab...

Malyla, V, De Rubis, G, Paudel, KR, Chellappan, DK, Hansbro, NG, Hansbro, PM & Dua, K 2023, 'Berberine nanostructures attenuate ß-catenin, a key component of epithelial mesenchymal transition in lung adenocarcinoma', Naunyn-Schmiedeberg's Archives of Pharmacology, vol. 396, no. 12, pp. 3595-3603.
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AbstractLung cancer (LC) is the leading cause of cancer-related deaths globally. It accounts for more than 1.9 million cases each year due to its complex and poorly understood molecular mechanisms that result in unregulated cell proliferation and metastasis. β-Catenin is a developmentally active protein that controls cell proliferation, metastasis, polarity and cell fate during homeostasis and aids in cancer progression via epithelial–mesenchymal transition. Therefore, inhibition of the β-catenin pathway could attenuate the progression of LC. Berberine, an isoquinoline alkaloid which is known for its anti-cancer and anti-inflammatory properties, demonstrates poor solubility and bioavailability. In our study, we have encapsulated berberine into liquid crystalline nanoparticles to improve its physiochemical functions and studied if these nanoparticles target the β-catenin pathway to inhibit the human lung adenocarcinoma cell line (A549) at both gene and protein levels. We observed for the first time that berberine liquid crystalline nanoparticles at 5 µM significantly attenuate the expression of the β-catenin gene and protein. The interaction between berberine and β-catenin was further validated by molecular simulation studies. Targeting β-catenin with berberine nanoparticles represents a promising strategy for the management of lung cancer progression.

Malyla, V, Paudel, KR, De Rubis, G, Hansbro, NG, Hansbro, PM & Dua, K 2023, 'Cigarette smoking induces lung cancer tumorigenesis via upregulation of the WNT/β-catenin signaling pathway', Life Sciences, vol. 326, pp. 121787-121787.
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Mao, S, Feng, A, Zhang, S, Onggowarsito, C, Chen, Q, Su, D & Fu, Q 2023, 'Investigation of structure–property–application relationships of a hydrogel-based solar vapor generator', Journal of Materials Chemistry A, vol. 11, no. 42, pp. 23062-23070.
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We correlated the hydration ability of different hydrophilic groups to the varying performance of their corresponding hydrogels in solar vapor generation (SVG), establishing the relationships between the chemical structure, hydration property, and applications.

Marlton, FP, Brown, AJ, Sale, M, Maljuk, A, Büchner, B, Lewis, W, Luck, I, Wood, ML, Mole, RA & Ling, CD 2023, 'Selective Interstitial Hydration Explains Anomalous Structural Distortions and Ionic Conductivity in 6H-Ba₄Ta₂O₉·1/2H₂O', Chemistry of Materials, vol. 35, no. 7, pp. 2740-2751.
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Masoumeh Ghorbanpour, S, Wen, S, Kaitu'u‐Lino, TJ, Hannan, NJ, Jin, D & McClements, L 2023, 'Quantitative Point of Care Tests for Timely Diagnosis of Early‐Onset Preeclampsia with High Sensitivity and Specificity', Angewandte Chemie, vol. 135, no. 26.
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AbstractPreeclampsia is a heterogeneous and multiorgan cardiovascular disorder of pregnancy. Here, we report the development of a novel strip‐based lateral flow assay (LFA) using lanthanide‐doped upconversion nanoparticles conjugated to antibodies targeting two different biomarkers for detection of preeclampsia. We first measured circulating plasma FKBPL and CD44 protein concentrations from individuals with early‐onset preeclampsia (EOPE), using ELISA. We confirmed that the CD44/FKBPL ratio is reduced in EOPE with a good diagnostic potential. Using our rapid LFA prototypes, we achieved an improved lower limit of detection: 10 pg ml−1 for FKBPL and 15 pg ml−1 for CD44, which is more than one order lower than the standard ELISA method. Using clinical samples, a cut‐off value of 1.24 for CD44/FKBPL ratio provided positive predictive value of 100 % and the negative predictive value of 91 %. Our LFA shows promise as a rapid and highly sensitive point‐of‐care test for preeclampsia.

Masoumeh Ghorbanpour, S, Wen, S, Kaitu'u‐Lino, TJ, Hannan, NJ, Jin, D & McClements, L 2023, 'Quantitative Point of Care Tests for Timely Diagnosis of Early‐Onset Preeclampsia with High Sensitivity and Specificity', Angewandte Chemie International Edition, vol. 62, no. 26.
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AbstractPreeclampsia is a heterogeneous and multiorgan cardiovascular disorder of pregnancy. Here, we report the development of a novel strip‐based lateral flow assay (LFA) using lanthanide‐doped upconversion nanoparticles conjugated to antibodies targeting two different biomarkers for detection of preeclampsia. We first measured circulating plasma FKBPL and CD44 protein concentrations from individuals with early‐onset preeclampsia (EOPE), using ELISA. We confirmed that the CD44/FKBPL ratio is reduced in EOPE with a good diagnostic potential. Using our rapid LFA prototypes, we achieved an improved lower limit of detection: 10 pg ml−1 for FKBPL and 15 pg ml−1 for CD44, which is more than one order lower than the standard ELISA method. Using clinical samples, a cut‐off value of 1.24 for CD44/FKBPL ratio provided positive predictive value of 100 % and the negative predictive value of 91 %. Our LFA shows promise as a rapid and highly sensitive point‐of‐care test for preeclampsia.

Massahud, E, Ahmed, H, Babarao, R, Ehrnst, Y, Alijani, H, Darmanin, C, Murdoch, BJ, Rezk, AR & Yeo, LY 2023, 'Acoustomicrofluidic Defect Engineering and Ligand Exchange in ZIF‐8 Metal–Organic Frameworks', Small Methods, vol. 7, no. 6.
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AbstractA way through which the properties of metal–organic frameworks (MOFs) can be tuned is by engineering defects into the crystal structure. Given its intrinsic stability and rigidity, however, it is difficult to introduce defects into zeolitic imidazolate frameworks (ZIFs)—and ZIF‐8, in particular—without compromising crystal integrity. In this work, it is shown that the acoustic radiation pressure as well as the hydrodynamic stresses arising from the oscillatory flow generated by coupling high frequency (MHz‐order) hybrid surface and bulk acoustic waves into a suspension of ZIF‐8 crystals in a liquid pressure transmitting medium is capable of driving permanent structural changes in their crystal lattice structure. Over time, the enhancement in the diffusive transport of guest molecules into the material's pores as a consequence is shown to lead to expansion of the pore framework, and subsequently, the creation of dangling‐linker and missing‐linker defects, therefore offering the possibility of tuning the type and extent of defects engineered into the MOF through the acoustic exposure time. Additionally, the practical utility of the technology is demonstrated for one‐pot, simultaneous solvent‐assisted ligand exchange under ambient conditions, for sub‐micron‐dimension ZIF‐8 crystals and relatively large ligands—more specifically 2‐aminobenzimidazole—without compromising the framework porosity or overall crystal structure.

Mata, L, Hahs, AK, Palma, E, Backstrom, A, Johnston, N, King, T, Olson, AR, Renowden, C, Smith, TR, Vogel, B & Ward, S 2023, 'Large positive ecological changes of small urban greening actions', Ecological Solutions and Evidence, vol. 4, no. 3.
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AbstractThe detrimental effects of environmental change on human and non‐human diversity are acutely manifested in urban environments. While urban greenspaces are known to mitigate these effects and support functionally diverse ecological communities, evidence of the ecological outcomes of urban greening remains scarce.We use a longitudinal observational design to provide empirical evidence of positive ecological changes brought about by greening actions. We collected a plant–insect interactions data set 1 year before, and for 3 years after, a greenspace received a small greening action within a densely urbanised municipality. We then assessed how (i) insect species richness; (ii) the probabilities of occurrence, survival and colonisation of the insect community; and (iii) the plant–insect network structure varied across the 4 years of the study. As we understand, this is the first study to apply statistical and network analytical frameworks to quantitatively track how positive ecological changes accrue over time at a site after the implementation of a specific urban greening action.We show how a small greening action quickly led to large positive changes in the richness, demographic dynamics and network structure of a depauperate insect community. An increase in the diversity and complexity of the plant community led to, after only 3 years, a large increase in insect species richness, a greater probability of occurrence of insects within the greenspace and a higher number and diversity of interactions between insects and plant species.We demonstrate how large positive ecological changes may be derived from investing in small greening actions and how these contribute to bring indigenous species back to greenspaces where they have ...

Matar, F, Shi, Y-L, Ling, FC-C, Salih, A, Irvine, CP, De Silva, S, Phillips, MR & Ton-That, C 2023, 'Bandgap narrowing and hole self-trapping reduction in Ga2O3 by Bi2O3 alloying', Journal of Alloys and Compounds, vol. 960, pp. 170983-170983.
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Matheson, S, Fleck, R, Irga, PJ & Torpy, FR 2023, 'Phytoremediation for the indoor environment: a state-of-the-art review', Reviews in Environmental Science and Bio/Technology, vol. 22, no. 1, pp. 249-280.
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AbstractPoor indoor air quality has become of particular concern within the built environment due to the time people spend indoors, and the associated health burden. Volatile organic compounds (VOCs) off-gassing from synthetic materials, nitrogen dioxide and harmful outdoor VOCs such benzene, toluene, ethyl-benzene and xylene penetrate into the indoor environment through ventilation and are the main contributors to poor indoor air quality with health effects. A considerable body of literature over the last four decades has demonstrate the removal of gaseous contaminants through phytoremediation, a technology that relies on plant material and technologies to remediate contaminated air streams. In this review we present a state-of-the-art on indoor phytoremediation over the last decade. Here we present a review of 38 research articles on both active and passive phytoremediation, and describe the specific chemical removal efficiency of different systems. The literature clearly indicates the efficacy of these systems for the removal of gaseous contaminants in the indoor environment, however it is evident that the application of phytoremediation technologies for research purposes in-situ is currently significantly under studied. In addition, it is common for research studies to assess the removal of single chemical species under controlled conditions, with little relevancy to real-world settings easily concluded. The authors therefore recommend that future phytoremediation research be conducted both in-situ and on chemical sources of a mixed nature, such as those experienced in the urban environment like petroleum vapour, vehicle emissions, and mixed synthetic furnishings off-gassing. The assessment of these systems both in static chambers for their theoretical performance, and in-situ for these mixed chemical sources is essential for the progres...

Matheson, S, Fleck, R, Lockwood, T, Gill, RL, Irga, PJ & Torpy, FR 2023, 'Fuelling phytoremediation: gasoline degradation by green wall systems—a case study', Environmental Science and Pollution Research, vol. 30, no. 56, pp. 118545-118555.
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AbstractThe capacity for indoor plants including green wall systems to remove specific volatile organic compounds (VOCs) is well documented in the literature; however under realistic settings, indoor occupants are exposed to a complex mixture of harmful compounds sourced from various emission sources. Gasoline vapour is one of the key sources of these emissions, with several studies demonstrating that indoor occupants in areas surrounding gasoline stations or with residentially attached garages are exposed to far higher concentrations of harmful VOCs. Here we assess the potential of a commercial small passive green wall system, commercially named the ‘LivePicture Go’ from Ambius P/L, Australia, to drawdown VOCs that comprise gasoline vapour, including total VOC (TVOC) removal and specific removal of individual speciated VOCs over time. An 8-h TVOC removal efficiency of 42.45% was achieved, along with the complete removal of eicosane, 1,2,3-trimethyl-benzene, and hexadecane. Further, the green wall also effectively reduced concentrations of a range of harmful benzene derivatives and other VOCs. These results demonstrate the potential of botanical systems to simultaneously remove a wide variety of VOCs, although future research is needed to improve upon and ensure efficiency of these systems over time and within practical applications.

Matthews, JL, Hoch, L, Raina, J-B, Pablo, M, Hughes, DJ, Camp, EF, Seymour, JR, Ralph, PJ, Suggett, DJ & Herdean, A 2023, 'Symbiodiniaceae photophysiology and stress resilience is enhanced by microbial associations', Scientific Reports, vol. 13, no. 1, p. 20724.
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AbstractSymbiodiniaceae form associations with extra- and intracellular bacterial symbionts, both in culture and in symbiosis with corals. Bacterial associates can regulate Symbiodiniaceae fitness in terms of growth, calcification and photophysiology. However, the influence of these bacteria on interactive stressors, such as temperature and light, which are known to influence Symbiodiniaceae physiology, remains unclear. Here, we examined the photophysiological response of two Symbiodiniaceae species (Symbiodinium microadriaticum and Breviolum minutum) cultured under acute temperature and light stress with specific bacterial partners from their microbiome (Labrenzia (Roseibium) alexandrii, Marinobacter adhaerens or Muricauda aquimarina). Overall, bacterial presence positively impacted Symbiodiniaceae core photosynthetic health (photosystem II [PSII] quantum yield) and photoprotective capacity (non-photochemical quenching; NPQ) compared to cultures with all extracellular bacteria removed, although specific benefits were variable across Symbiodiniaceae genera and growth phase. Symbiodiniaceae co-cultured with M. aquimarina displayed an inverse NPQ response under high temperatures and light, and those with L. alexandrii demonstrated a lowered threshold for induction of NPQ, potentially through the provision of antioxidant compounds such as zeaxanthin (produced by Muricauda spp.) and dimethylsulfoniopropionate (DMSP; produced by this strain of L. alexandrii). Our co-culture approach empirically demonstrates the benefits bacteria can deliver to Symbiodiniaceae photochemical performance, providing evidence tha...

Matthews, JL, Khalil, A, Siboni, N, Bougoure, J, Guagliardo, P, Kuzhiumparambil, U, DeMaere, M, Le Reun, NM, Seymour, JR, Suggett, DJ & Raina, J-B 2023, 'Coral endosymbiont growth is enhanced by metabolic interactions with bacteria', Nature Communications, vol. 14, no. 1, p. 6864.
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AbstractBacteria are key contributors to microalgae resource acquisition, competitive performance, and functional diversity, but their potential metabolic interactions with coral microalgal endosymbionts (Symbiodiniaceae) have been largely overlooked. Here, we show that altering the bacterial composition of two widespread Symbiodiniaceae species, during their free-living stage, results in a significant shift in their cellular metabolism. Indeed, the abundance of monosaccharides and the key phytohormone indole-3-acetic acid (IAA) were correlated with the presence of specific bacteria, including members of the Labrenzia (Roseibium) and Marinobacter genera. Single-cell stable isotope tracking revealed that these two bacterial genera are involved in reciprocal exchanges of carbon and nitrogen with Symbiodiniaceae. We identified the provision of IAA by Labrenzia and Marinobacter, and this metabolite caused a significant growth enhancement of Symbiodiniaceae. By unravelling these interkingdom interactions, our work demonstrates how specific bacterial associates fundamentally govern Symbiodiniaceae fitness.

McDonald, VM, Archbold, G, Beyene, T, Brew, BK, Franklin, P, Gibson, PG, Harrington, J, Hansbro, PM, Johnston, FH, Robinson, PD, Sutherland, M, Yates, D, Zosky, GR & Abramson, MJ 2023, 'Asthma and landscape fire smoke: A Thoracic Society of Australia and New Zealand position statement', Respirology, vol. 28, no. 11, pp. 1023-1035.
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AbstractLandscape fires are increasing in frequency and severity globally. In Australia, extreme bushfires cause a large and increasing health and socioeconomic burden for communities and governments. People with asthma are particularly vulnerable to the effects of landscape fire smoke (LFS) exposure. Here, we present a position statement from the Thoracic Society of Australia and New Zealand. Within this statement we provide a review of the impact of LFS on adults and children with asthma, highlighting the greater impact of LFS on vulnerable groups, particularly older people, pregnant women and Aboriginal and Torres Strait Islander peoples. We also highlight the development of asthma on the background of risk factors (smoking, occupation and atopy). Within this document we present advice for asthma management, smoke mitigation strategies and access to air quality information, that should be implemented during periods of LFS. We promote clinician awareness, and the implementation of public health messaging and preparation, especially for people with asthma.

McNaughton, DA, Ryder, WG, Gilchrist, AM, Wang, P, Fares, M, Wu, X & Gale, PA 2023, 'New insights and discoveries in anion receptor chemistry', Chem, vol. 9, no. 11, pp. 3045-3112.
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This review offers a broad overview of the advancements in anion receptor chemistry in 2021 and 2022. Detailed examples of acclaimed work in fundamental recognition, sensing and detection, catalysis, self-assembly, extraction, and transmembrane transport are included.

McNeilly, O, Mann, R, Cummins, ML, Djordjevic, SP, Hamidian, M & Gunawan, C 2023, 'Development of Nanoparticle Adaptation Phenomena in Acinetobacter baumannii: Physiological Change and Defense Response', Microbiology Spectrum, vol. 11, no. 1, p. e0285722.
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Several recent studies have reported on the development of bacterial resistance to broad-spectrum antimicrobial silver nanoparticles (nanosilver; NAg). NAg is currently one of the most important alternative antimicrobial agents.

Mehta, M, Bui, TA, Yang, X, Aksoy, Y, Goldys, EM & Deng, W 2023, 'Lipid-Based Nanoparticles for Drug/Gene Delivery: An Overview of the Production Techniques and Difficulties Encountered in Their Industrial Development', ACS Materials Au, vol. 3, no. 6, pp. 600-619.
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Mello, MG, Westerhausen, MT, Lockwood, TE, Singh, P, Wanagat, J & Bishop, DP 2023, 'Immunolabelling perturbs the endogenous and antibody-conjugated elemental concentrations during immuno-mass spectrometry imaging', Analytical and Bioanalytical Chemistry.
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AbstractImmuno-mass spectrometry imaging uses lanthanide-conjugated antibodies to spatially quantify biomolecules via laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). The multi-element capabilities allow for highly multiplexed analyses that may include both conjugated antibodies and endogenous metals to reveal relationships between disease and chemical composition. Sample handling is known to perturb the composition of the endogenous elements, but there has been little investigation into the effects of immunolabelling and coverslipping. Here, we used cryofixed muscle sections to examine the impact of immunolabelling steps on the concentrations of a Gd-conjugated anti-dystrophin primary antibody, and the endogenous metals Cu and Zn. Primary antibody incubation resulted in a decrease in Zn, and an increase in Cu. Zn was removed from the cytoplasm where it was hypothesised to be more labile, whereas concentrated locations of Zn remained in the cell membrane in all samples that underwent the immunostaining process. Cu increased in concentration and was found mostly in the cell membrane. The concentration of the Gd-conjugated antibody when compared to the standard air-dried sample was not significantly different when coverslipped using an organic mounting medium, whereas use of an aqueous mounting medium significantly reduced the concentration of Gd. These results build on the knowledge of how certain sample handling techniques change elemental concentrations and distributions in tissue sections. Immunolabelling steps impact the concentration of endogenous elements, and separate histological sections are required for the quantitative analysis of endogenous elements and biomolecules. Additionally, coverslipping tissue sections for complementary immunohistochemical/immunofluorescent imaging may compromise the integrity of the elemental label, and organic mounting media are recommended over aqueous mounti...

Mendes de Almeida, V, Engel, DF, Ricci, MF, Cruz, CS, Lopes, ÍS, Alves, DA, d’ Auriol, M, Magalhães, J, Machado, EC, Rocha, VM, Carvalho, TG, Lacerda, LSB, Pimenta, JC, Aganetti, M, Zuccoli, GS, Smith, BJ, Carregari, VC, da Silva Rosa, E, Galvão, I, Dantas Cassali, G, Garcia, CC, Teixeira, MM, André, LC, Ribeiro, FM, Martins, FS, Saia, RS, Costa, VV, Martins-de-Souza, D, Hansbro, PM, Marques, JT, Aguiar, ERGR & Vieira, AT 2023, 'Gut microbiota from patients with COVID-19 cause alterations in mice that resemble post-COVID symptoms', Gut Microbes, vol. 15, no. 2, p. 2249146.
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Long-term sequelae of coronavirus disease (COVID)-19 are frequent and of major concern. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection affects the host gut microbiota, which is linked to disease severity in patients with COVID-19. Here, we report that the gut microbiota of post-COVID subjects had a remarkable predominance of Enterobacteriaceae strains with an antibiotic-resistant phenotype compared to healthy controls. Additionally, short-chain fatty acid (SCFA) levels were reduced in feces. Fecal transplantation from post-COVID subjects to germ-free mice led to lung inflammation and worse outcomes during pulmonary infection by multidrug-resistant Klebsiella pneumoniae. transplanted mice also exhibited poor cognitive performance. Overall, we show prolonged impacts of SARS-CoV-2 infection on the gut microbiota that persist after subjects have cleared the virus. Together, these data demonstrate that the gut microbiota can directly contribute to post-COVID sequelae, suggesting that it may be a potential therapeutic target.

Menictas, M, Di Credico, G & Wand, MP 2023, 'Streamlined Variational Inference for Linear Mixed Models with Crossed Random Effects', Journal of Computational and Graphical Statistics, vol. 32, no. 1, pp. 99-115.
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Mercer-Mapstone, L, Banas, K, Davila, Y, Huston, W, Meier, P & Mekonnen, B 2023, '‘I’m not alone’: outcomes of a faculty-wide initiative for co-creating inclusive science curricula through student–staff partnership', International Journal for Academic Development, vol. 28, no. 2, pp. 149-162.
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Mercieca, AL, Fursman, HC, Alonzo, M, Chadwick, S & McDonagh, AM 2023, 'Organic impurity profiling of 3,4-methylenedioxyamphetamine (MDA) synthesised from helional', Forensic Science International, vol. 350, pp. 111788-111788.
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Mi, C, Zhang, X, Yang, C, Wu, J, Chen, X, Ma, C, Wu, S, Yang, Z, Qiao, P, Liu, Y, Wu, W, Guo, Z, Liao, J, Zhou, J, Guan, M, Liang, C, Liu, C & Jin, D 2023, 'Bone disease imaging through the near-infrared-II window', Nature Communications, vol. 14, no. 1, p. 6287.
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AbstractSkeletal disorders are commonly diagnosed by X-ray imaging, but the radiation limits its use. Optical imaging through the near-infrared-II window (NIR-II, 1000–1700 nm) can penetrate deep tissues without radiation risk, but the targeting of contrast agent is non-specific. Here, we report that lanthanide-doped nanocrystals can passively target the bone marrow, which can be effective for over two months. We therefore develop the high-resolution NIR-II imaging method for bone disease diagnosis, including the 3D bone imaging instrumentation to show the intravital bone morphology. We demonstrate the monitoring of 1 mm bone defects with spatial resolution comparable to the X-ray imaging result. Moreover, NIR-II imaging can reveal the early onset inflammation as the synovitis in the early stage of rheumatoid arthritis, comparable to micro computed tomography (μCT) in diagnosis of osteoarthritis, including the symptoms of osteophyte and hyperostosis in the knee joint.

Milner, KV, French, K, Krix, DW, Valenzuela, SM & Leigh, A 2023, 'The effects of spring versus summer heat events on two arid zone plant species under field conditions', Functional Plant Biology, vol. 50, no. 6, pp. 455-469.
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Heatwaves are increasingly occurring out-of-season, which may affect plants not primed for the event. Further, heat stress often coincides with water and/or nutrient stress, impairing short-term physiological function and potentially causing downstream effects on reproductive fitness. We investigated the response of water-stressed arid-zone Solanum oligacanthum and Solanum orbiculatum to spring vs summer heat stress under differing nutrient conditions. Heat stress events were imposed in open-topped chambers under in situ desert conditions. To assess short-term impacts, we measured leaf photosystem responses (Fv/Fm) and membrane stability; long-term effects were compared via biomass allocation, visible damage, flowering and fruiting. Plants generally fared more poorly following summer than spring heat stress, with the exception of Fv/Fm. Summer heat stress caused greater membrane damage, reduced growth and survival compared with spring. Nutrient availability had a strong influence on downstream effects of heat stress, including species-specific outcomes for reproductive fitness. Overall, high temperatures during spring posed a lower threat to fitness than in severe arid summer conditions of high temperature and low water availability, which were more detrimental to plants in both the short and longer term. Our study highlights the importance of considering ecologically relevant, multiple-stressor events to understand different species responses to extreme heat.

Minzière, VR, Gassner, A, Gallidabino, M, Roux, C & Weyermann, C 2023, 'The relevance of gunshot residues in forensic science', WIREs Forensic Science, vol. 5, no. 1.
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AbstractGunshot residues (GSR) are routinely exploited by forensic scientists in the investigation of firearm‐related events. While many new techniques are daily reported in the literature for the analysis of GSR, there is still a significant lack of data on the transfer, persistence, and prevalence of GSR. Such fundamental knowledge is essential to fully exploit the information potential of GSR for investigation or in Court. This article provides an overview of the relevant questions related to GSR, more particularly to infer about the trace's origin (i.e., is it from a firearm discharge?) and the activity that caused transfer (e.g., primary, secondary, or subsequent transfer). GSR production and composition will be briefly described, considering both inorganic and organic components. Then, the available knowledge about the primary transfer, the secondary transfer, and the persistence of GSR will be outlined, as well as the prevalence (background level) of the targeted elements and/or compounds in the environment, more particularly on the hands of people unrelated to firearm incidents. Finally, the methods developed for the collection, analysis, and interpretation of GSR will be discussed. A holistic approach combining fundamental forensic science knowledge about GSR transfer, persistence, and prevalence together with other available information is discussed as a path forward to increase the relevance and value of the GSR trace in practice.This article is categorized under:Crime Scene Investigation > From Traces to Intelligence and EvidenceForensic Chemistry and Trace Evidence > Trace EvidenceForensic Chemistry and Trace Evidence > Explosive Analysis

Mirakhorli, F, Razavi Bazaz, S, Warkiani, ME & Ralph, PJ 2023, 'Ultra-high throughput microfluidic concentrator for harvesting of Tetraselmis sp. (Chlorodendrophyceae, Chlorophyta)', Algal Research, vol. 72, pp. 103145-103145.
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Mitchell, A, Hayes, C, Booth, DJ & Nagelkerken, I 2023, 'Future shock: Ocean acidification and seasonal water temperatures alter the physiology of competing temperate and coral reef fishes', Science of The Total Environment, vol. 883, pp. 163684-163684.
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Mitchell, A, Hayes, C, Booth, DJ & Nagelkerken, I 2023, 'Projected ocean acidification and seasonal temperature alter the behaviour and growth of a range extending tropical fish', Coral Reefs, vol. 42, no. 4, pp. 919-929.
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AbstractClimate-driven invasions of ecosystems by range-extending animals are often mediated by behavioural modifications that increase their chances of establishment in foreign biological communities. This creates novel ecological interactions that can affect the behaviour of native species in recipient ecosystems. However, this question has seldom been addressed in marine systems, in particular with the additive effect of ocean acidification and the mediating effects of seasonal climate variability. Here, we performed a laboratory experiment to evaluate how novel species interactions, ocean acidification, and projected future summer versus winter temperatures could affect the behaviour and growth of a range-extending tropical and co-shoaling temperate fish. Compared to current-day summer temperatures, tropical fish became 4% more active, 90% more aggressive, and increased their growth rates (standard length: +42%) during future summers in their novel poleward ranges, but reduced their aggression by 64%, boldness by 52%, feeding by 45% and growth rates (wet weight: −70%, standard length: −26%) during future winters compared to current-day summer temperatures. Additionally, tropical fish became 3% more active under ocean acidification compared to no ocean acidification. Conversely, temperate fish behaviour was unaffected by climate treatments but their growth rates were > 200% faster under future winter versus current and future summer temperatures. We conclude that projected future winter conditions in temperate ecosystems may reduce the performance of range-extending fishes in temperate fish communities and slow down tropicalisation of higher latitudes.

Mohkam, M, Sadraeian, M, Lauto, A, Gholami, A, Nabavizadeh, SH, Esmaeilzadeh, H & Alyasin, S 2023, 'Exploring the potential and safety of quantum dots in allergy diagnostics', Microsystems & Nanoengineering, vol. 9, no. 1, p. 145.
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AbstractBiomedical investigations in nanotherapeutics and nanomedicine have recently intensified in pursuit of new therapies with improved efficacy. Quantum dots (QDs) are promising nanomaterials that possess a wide array of advantageous properties, including electronic properties, optical properties, and engineered biocompatibility under physiological conditions. Due to these characteristics, QDs are mainly used for biomedical labeling and theranostic (therapeutic-diagnostic) agents. QDs can be functionalized with ligands to facilitate their interaction with the immune system, specific IgE, and effector cell receptors. However, undesirable side effects such as hypersensitivity and toxicity may occur, requiring further assessment. This review systematically summarizes the potential uses of QDs in the allergy field. An overview of the definition and development of QDs is provided, along with the applications of QDs in allergy studies, including the detection of allergen-specific IgE (sIgE), food allergens, and sIgE in cellular tests. The potential treatment of allergies with QDs is also described, highlighting the toxicity and biocompatibility of these nanodevices. Finally, we discuss the current findings on the immunotoxicity of QDs. Several favorable points regarding the use of QDs for allergy diagnosis and treatment are noted.

Momtazmanesh, S, Moghaddam, SS, Ghamari, S-H, Rad, EM, Rezaei, N, Shobeiri, P, Aali, A, Abbasi-Kangevari, M, Abbasi-Kangevari, Z, Abdelmasseh, M, Abdoun, M, Abdulah, DM, Md Abdullah, AY, Abedi, A, Abolhassani, H, Abrehdari-Tafreshi, Z, Achappa, B, Adane Adane, DE, Adane, TD, Addo, IY, Adnan, M, Sakilah Adnani, QE, Ahmad, S, Ahmadi, A, Ahmadi, K, Ahmed, A, Ahmed, A, Rashid, TA, Al Hamad, H, Alahdab, F, Alemayehu, A, Alif, SM, Aljunid, SM, Almustanyir, S, Altirkawi, KA, Alvis-Guzman, N, Dehkordi, JA, Amir-Behghadami, M, Ancuceanu, R, Andrei, CL, Andrei, T, Antony, CM, Anyasodor, AE, Arabloo, J, Arulappan, J, Ashraf, T, Athari, SS, Attia, EF, Ayele, MT, Azadnajafabad, S, Babu, AS, Bagherieh, S, Baltatu, OC, Banach, M, Bardhan, M, Barone-Adesi, F, Barrow, A, Basu, S, Bayileyegn, NS, Bensenor, IM, Bhardwaj, N, Bhardwaj, P, Bhat, AN, Bhattacharyya, K, Bouaoud, S, Braithwaite, D, Brauer, M, Butt, MH, Butt, ZA, Calina, D, Cámera, LA, Chanie, GS, Charalampous, P, Chattu, VK, Chimed-Ochir, O, Chu, D-T, Cohen, AJ, Cruz-Martins, N, Dadras, O, Darwesh, AM, Das, S, Debela, SA, Delgado-Ortiz, L, Dereje, D, Dianatinasab, M, Diao, N, Diaz, D, Digesa, LE, Dirirsa, G, Doku, PN, Dongarwar, D, Douiri, A, Dsouza, HL, Eini, E, Ekholuenetale, M, Ekundayo, TC, Mustafa Elagali, AE, Elhadi, M, Enyew, DB, Erkhembayar, R, Etaee, F, Fagbamigbe, AF, Faro, A, Fatehizadeh, A, Fekadu, G, Filip, I, Fischer, F, Foroutan, M, Franklin, RC, Gaal, PA, Gaihre, S, Gaipov, A, Gebrehiwot, M, Gerema, U, Getachew, ME, Getachew, T, Ghafourifard, M, Ghanbari, R, Ghashghaee, A, Gholami, A, Gil, AU, Golechha, M, Goleij, P, Golinelli, D, Guadie, HA, Gupta, B, Gupta, S, Gupta, VB, Gupta, VK, Hadei, M, Halwani, R, Hanif, A, Hargono, A, Harorani, M, Hartono, RK, Hasani, H, Hashi, A, Hay, SI, Heidari, M, Hellemons, ME, Herteliu, C, Holla, R, Horita, N, Hoseini, M, Hosseinzadeh, M, Huang, J, Hussain, S, Hwang, B-F, Iavicoli, I, Ibitoye, SE, Ibrahim, S, Ilesanmi, OS, Ilic, IM, Ilic, MD, Immurana, M, Ismail, NE, Merin J, L, Jakovljevic, M, Jamshidi, E, Janodia, MD, Javaheri, T, Jayapal, SK, Jayaram, S, Jha, RP, Johnson, O, Joo, T, Joseph, N, Jozwiak, JJ, K, V, Kaambwa, B, Kabir, Z, Kalankesh, LR, Kalhor, R, Kandel, H, Karanth, SD, Karaye, IM, Kassa, BG, Kassie, GM, Keikavoosi-Arani, L, Keykhaei, M, Khajuria, H, Khan, IA, Khan, MAB, Khan, YH, Khreis, H, Kim, MS, Kisa, A, Kisa, S & et al. 2023, 'Global burden of chronic respiratory diseases and risk factors, 1990–2019: an update from the Global Burden of Disease Study 2019', eClinicalMedicine, vol. 59, pp. 101936-101936.
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BACKGROUND: Updated data on chronic respiratory diseases (CRDs) are vital in their prevention, control, and treatment in the path to achieving the third UN Sustainable Development Goals (SDGs), a one-third reduction in premature mortality from non-communicable diseases by 2030. We provided global, regional, and national estimates of the burden of CRDs and their attributable risks from 1990 to 2019. METHODS: Using data from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019, we estimated mortality, years lived with disability, years of life lost, disability-adjusted life years (DALYs), prevalence, and incidence of CRDs, i.e. chronic obstructive pulmonary disease (COPD), asthma, pneumoconiosis, interstitial lung disease and pulmonary sarcoidosis, and other CRDs, from 1990 to 2019 by sex, age, region, and Socio-demographic Index (SDI) in 204 countries and territories. Deaths and DALYs from CRDs attributable to each risk factor were estimated according to relative risks, risk exposure, and the theoretical minimum risk exposure level input. FINDINGS: In 2019, CRDs were the third leading cause of death responsible for 4.0 million deaths (95% uncertainty interval 3.6-4.3) with a prevalence of 454.6 million cases (417.4-499.1) globally. While the total deaths and prevalence of CRDs have increased by 28.5% and 39.8%, the age-standardised rates have dropped by 41.7% and 16.9% from 1990 to 2019, respectively. COPD, with 212.3 million (200.4-225.1) prevalent cases, was the primary cause of deaths from CRDs, accounting for 3.3 million (2.9-3.6) deaths. With 262.4 million (224.1-309.5) prevalent cases, asthma had the highest prevalence among CRDs. The age-standardised rates of all burden measures of COPD, asthma, and pneumoconiosis have reduced globally from 1990 to 2019. Nevertheless, the age-standardised rates of incidence and prevalence of interstitial lung disease and pulmonary sarcoidosis have increased throughout this period. Low- and lo...

Moneer, EA, Bakr, BA, Akl, SH, Shahin, YH, Elwakil, BH, Hagar, M, Paudel, KR, Aljuhani, A, Aouad, MR & Rezki, N 2023, 'Design and synthesis of novel bis-pyridinium based-ionic liquids as potent antiparasitic agents', Heliyon, vol. 9, no. 4, pp. e15431-e15431.
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Moore, SJ, Deplazes, E & Mancera, RL 2023, 'Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide', Proteins: Structure, Function, and Bioinformatics, vol. 91, no. 3, pp. 338-353.
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AbstractHuman islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein (IDP) whose abnormal aggregation into toxic soluble oligomers and insoluble amyloid fibrils is a pathological feature in type‐2 diabetes. Rat IAPP (rIAPP) differs from hIAPP by only six amino acids yet has a reduced tendency to aggregate or form fibrils. The structures of the monomeric forms of IAPP are difficult to characterize due to their intrinsically disordered nature. Molecular dynamics simulations can provide a detailed characterization of the monomeric forms of rIAPP and hIAPP in near‐physiological conditions. In this work, the conformational landscapes of rIAPP and hIAPP as a function of secondary structure content were predicted using well‐tempered bias exchange metadynamics simulations. Several combinations of commonly used biomolecular force fields and water models were tested. The predicted conformational preferences of both rIAPP and hIAPP are typical of IDPs, exhibiting dominant random coil structures but showing a low propensity for transient α‐helical conformations. Predicted nuclear magnetic resonance Cα chemical shifts reveal different preferences with each force field towards certain conformations, with AMBERff99SBnmr2/TIP4Pd showing the best agreement with the experiment. Comparisons of secondary structure content demonstrate residue‐specific differences between hIAPP and rIAPP that may reflect their different aggregation propensities.

Moraleda Merlo, AB, Roux, C, Bécue, A & Weyermann, C 2023, 'A comparison of the natural and groomed fingermark lipid composition of different donors using GC/MS', Forensic Science International, vol. 348, pp. 111709-111709.
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Morel, J, McNeilly, O, Grundy, S, Brown, T, Gunawan, C, Amal, R & Scott, JA 2023, 'Nanoscale Titanium Surface Engineering via Low-Temperature Hydrothermal Etching for Enhanced Antimicrobial Properties', ACS Applied Materials & Interfaces, vol. 15, no. 39, pp. 46247-46260.
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Bioinspired nanotopography artificially fabricated on titanium surfaces offers a solution for the rising issue of postoperative infections within orthopedics. On a small scale, hydrothermal etching has proven to deliver an effective antimicrobial nanospike surface. However, translation to an industrial setting is limited by the elevated synthesis temperature (150 °C) and associated equipment requirements. Here, for the first time, we fabricate surface nanostructures using comparatively milder synthesis temperatures (75 °C), which deliver physicochemical properties and antimicrobial capability comparable to the high-temperature surface. Using a KOH etchant, the simultaneous formation of titania and titanate crystals at both temperatures produces a one-dimensional nanostructure array. Analysis indicated that the formation mechanism comprises dissolution and reprecipitation processes, identifying the deposited titanates as hydrated layered tetra-titanates (K2Ti4O9·nH2O). A proposed nanospike formation mechanism was confirmed through the identification of a core and outer shell for individual nanostructures, primarily comprised of titanates and titania, respectively. Etching conditions dictated crystalline formation, favoring a thicker titanate core for nanorods under higher synthesis temperatures and etchant concentrations. A bactericidal investigation showed the efficacy against Gram-negative bacteria for a representative low-temperature nanosurface (34.4 ± 14.4%) was comparable to the higher temperature nanosurface (34.0 ± 17.0%), illustrating the potential of low-temperature hydrothermal synthesis. Our results provide valuable insight into the applicability of low-temperature etching protocols that are more favorable in large-scale manufacturing settings.

Morshedi Rad, D, Hansen, WP, Zhand, S, Cranfield, C & Ebrahimi Warkiani, M 2023, 'A hybridized mechano-electroporation technique for efficient immune cell engineering', Journal of Advanced Research.
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Mu, A, Klare, WP, Baines, SL, Ignatius Pang, CN, Guérillot, R, Harbison-Price, N, Keller, N, Wilksch, J, Nhu, NTK, Phan, M-D, Keller, B, Nijagal, B, Tull, D, Dayalan, S, Chua, HHC, Skoneczny, D, Koval, J, Hachani, A, Shah, AD, Neha, N, Jadhav, S, Partridge, SR, Cork, AJ, Peters, K, Bertolla, O, Brouwer, S, Hancock, SJ, Álvarez-Fraga, L, De Oliveira, DMP, Forde, B, Dale, A, Mujchariyakul, W, Walsh, CJ, Monk, I, Fitzgerald, A, Lum, M, Correa-Ospina, C, Roy Chowdhury, P, Parton, RG, De Voss, J, Beckett, J, Monty, F, McKinnon, J, Song, X, Stephen, JR, Everest, M, Bellgard, MI, Tinning, M, Leeming, M, Hocking, D, Jebeli, L, Wang, N, Ben Zakour, N, Yasar, SA, Vecchiarelli, S, Russell, T, Zaw, T, Chen, T, Teng, D, Kassir, Z, Lithgow, T, Jenney, A, Cole, JN, Nizet, V, Sorrell, TC, Peleg, AY, Paterson, DL, Beatson, SA, Wu, J, Molloy, MP, Syme, AE, Goode, RJA, Hunter, AA, Bowland, G, West, NP, Wilkins, MR, Djordjevic, SP, Davies, MR, Seemann, T, Howden, BP, Pascovici, D, Tyagi, S, Schittenhelm, RB, De Souza, DP, McConville, MJ, Iredell, JR, Cordwell, SJ, Strugnell, RA, Stinear, TP, Schembri, MA & Walker, MJ 2023, 'Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria', Nature Communications, vol. 14, no. 1, p. 1530.
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AbstractEven in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20–40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection. In addition, acquisition of cholesterol was identified across the bacterial species. This detailed reference dataset has been established as an open resource to support discovery and translational research.

Mugunthan, S, Wong, LL, Winnerdy, FR, Summers, S, Bin Ismail, MH, Foo, YH, Jaggi, TK, Meldrum, OW, Tiew, PY, Chotirmall, SH, Rice, SA, Phan, AT, Kjelleberg, S & Seviour, T 2023, 'RNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms', Nature Communications, vol. 14, no. 1, p. 7772.
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AbstractThe extracellular matrix of bacterial biofilms consists of diverse components including polysaccharides, proteins and DNA. Extracellular RNA (eRNA) can also be present, contributing to the structural integrity of biofilms. However, technical difficulties related to the low stability of RNA make it difficult to understand the precise roles of eRNA in biofilms. Here, we show that eRNA associates with extracellular DNA (eDNA) to form matrix fibres in Pseudomonas aeruginosa biofilms, and the eRNA is enriched in certain bacterial RNA transcripts. Degradation of eRNA associated with eDNA led to a loss of eDNA fibres and biofilm viscoelasticity. Compared with planktonic and biofilm cells, the biofilm matrix was enriched in specific mRNA transcripts, including lasB (encoding elastase). The mRNA transcripts colocalised with eDNA fibres in the biofilm matrix, as shown by single molecule inexpensive FISH microscopy (smiFISH). The lasB mRNA was also observed in eDNA fibres in a clinical sputum sample positive for P. aeruginosa. Thus, our results indicate that the interaction of specific mRNAs with eDNA facilitates the formation of viscoelastic networks in the matrix of Pseudomonas aeruginosa biofilms.

Muhammad, I, Ahmed, S, Cao, H, Mahmood, A & Wang, Y-G 2023, 'Three-Dimensional Silicene-Based Materials: A Universal Anode for Monovalent and Divalent Ion Batteries', The Journal of Physical Chemistry C, vol. 127, no. 2, pp. 1198-1208.
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Muhammad, I, Ahmed, S, Cao, H, Yao, Z, Khan, D, Mahmood, A, Hussain, T, Xiong, X-G, Ahuja, R & Wang, Y-G 2023, '3D porous sulfur-graphdiyne with splendid electrocatalytic and energy storage application', Materials Today Chemistry, vol. 34, pp. 101756-101756.
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Mullens, BG, Nicholas, MK, Marlton, FP, Brand, HEA, Gu, Q, Maynard-Casely, HE & Kennedy, BJ 2023, 'Long-range A-site cation disorder in NaA(MO4)2 (M = Mo, W) double scheelite oxides', Journal of Solid State Chemistry, vol. 321, pp. 123871-123871.
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Mullens, BG, Saura-Múzquiz, M, Marlton, FP, Avdeev, M, Brand, HEA, Mondal, S, Vaitheeswaran, G & Kennedy, BJ 2023, 'Beyond the ionic radii: A multifaceted approach to understand differences between the structures of LnNbO4 and LnTaO4 fergusonites', Journal of Alloys and Compounds, vol. 930, pp. 167399-167399.
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Murray, BR, Hawthorne, T, Curran, TJ, Krix, DW, Wallace, MI, Young, K, Murray, ML, Morley, E, Huber-Smith, N & Webb, JK 2023, 'Shoot flammability patterns among plant species of the wildland–urban interface in the fire-prone Greater Blue Mountains World Heritage Area', International Journal of Wildland Fire, vol. 32, no. 7, pp. 1119-1134.
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Background Mitigation of wildfires at the wildland–urban interface (WUI) will be enhanced by understanding the flammability of plants growing in this zone. Aims We aimed to: (1) compare shoot flammability among wildland native, and both urban native and urban exotic ornamental plants; (2) quantify relationships between shoot traits and flammability; and (3) establish flammability scores to distinguish low- from high-flammability species. Methods Flammability and traits of field-collected shoots were measured and relationships quantified in 44 species from the Blue Mountains World Heritage Area, Australia. Key results In our study area, urban exotic plants were less flammable than wildland and urban native plants. Slow-igniting shoots had high fuel moisture and bulk density; short-burning shoots had low bulk density and volume; shoots recording low maximum temperatures had high fuel moisture, low bulk density and volume; and shoots with low biomass consumed in flames had high fuel moisture and low volume. Our novel flammability scores distinguished low-flammability (e.g. Lophostemon confertus) from high-flammability native species (e.g. Callistemon citrinus). Conclusions and implications Low-flammability plantings at the WUI should preferably use native species given potential ecological impacts of exotics. We suggest that future work should seek to identify broader suites of low-flammability native species.

Murrihy, RC, Drysdale, SAO, Dedousis-Wallace, A, Rémond, L, McAloon, J, Ellis, DM, Halldorsdottir, T, Greene, RW & Ollendick, TH 2023, 'Community-Delivered Collaborative and Proactive Solutions and Parent Management Training for Oppositional Youth: A Randomized Trial', Behavior Therapy, vol. 54, no. 2, pp. 400-417.
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Nazari, H, Shrestha, J, Naei, VY, Bazaz, SR, Sabbagh, M, Thiery, JP & Warkiani, ME 2023, 'Advances in TEER measurements of biological barriers in microphysiological systems', Biosensors and Bioelectronics, vol. 234, pp. 115355-115355.
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Nguyen, HM, Ruocco, M, Dattolo, E, Cassetti, FP, Calvo, S, Tomasello, A, Marín‐Guirao, L, Pernice, M & Procaccini, G 2023, 'Signs of local adaptation by genetic selection and isolation promoted by extreme temperature and salinity in the Mediterranean seagrass Posidonia oceanica', Molecular Ecology, vol. 32, no. 15, pp. 4313-4328.
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AbstractAdaptation to local conditions is known to occur in seagrasses; however, knowledge of the genetic basis underlying this phenomenon remains scarce. Here, we analysed Posidonia oceanica from six sites within and around the Stagnone di Marsala, a semi‐enclosed coastal lagoon where salinity and temperature exceed the generally described tolerance thresholds of the species. Sea surface temperatures (SSTs) were measured and plant samples were collected for the assessment of morphology, flowering rate and for screening genome‐wide polymorphisms using double digest restriction‐site‐associated DNA sequencing. Results demonstrated more extreme SSTs and salinity levels inside the lagoon than the outer lagoon regions. Morphological results showed significantly fewer and shorter leaves and reduced rhizome growth of P. oceanica from the inner lagoon and past flowering events were recorded only for a meadow farthest away from the lagoon. Using an array of 51,329 single nucleotide polymorphisms, we revealed a clear genetic structure among the study sites and confirmed the genetic isolation and high clonality of the innermost site. In all, 14 outlier loci were identified and annotated with several proteins including those relate to plant stress response, protein transport and regulators of plant‐specific developmental events. Especially, five outlier loci showed maximum allele frequency at the innermost site, likely reflecting adaptation to the extreme temperature and salinity regimes, possibly due to the selection of more resistant genotypes and the progressive restriction of gene flow. Overall, this study helps us to disentangle the genetic basis of seagrass adaptation to local environmental conditions and may support future works on assisted evolution in seagrasses.

Nguyen, LN, Vu, MT, Vu, HP, Johir, MAH, Labeeuw, L, Ralph, PJ, Mahlia, TMI, Pandey, A, Sirohi, R & Nghiem, LD 2023, 'Microalgae-based carbon capture and utilization: A critical review on current system developments and biomass utilization', Critical Reviews in Environmental Science and Technology, vol. 53, no. 2, pp. 216-238.
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Carbon capture and utilization (CCU) is an emerging technology with commercial potential to convert atmospheric carbon dioxide (CO2) into net zero or negative emission products. In microalgae-based CCU, microalgae utilize CO2 and sunlight to generate biomass for commercial applications. This paper reviews the current state of microalgal culture development for CCU and highlights its potential contribution to addressing climate change challenges. Current microalgal culture systems have not been designed for high throughput biomass growth and carbon capture. Raceways, high-rate algal ponds, and photobioreactors are the most widely used for microalgal cultivation at a large-scale. The limitations of these systems are related to microalgal growth requirements. Ponds are operated at narrow depth to ensure sufficient light distribution and thus need a large land surface. CO2 gas needs to be in a dissolved form for efficient utilization by microalgae. Innovative system designs to achieve optimized distribution of light, nutrient, and CO2 utilization for enhanced biomass production are crucial to achieve large-scale CO2 capture by microalgae. Data corroborated in this review highlights several innovative techniques to deliver CO2 effectively and enhance light illumination to microalgal cells. Submerged and internal illuminations can enhance light distribution without compromising culture volume and land requirements. CO2 delivery technique selections mainly depend on CO2 sources. The carbonation column appears to be the best option regarding efficiency, easy operation, and simple design. The downstream processes of microalgal culture (i.e. harvesting, biomass utilization, and water reuse) are important to make microalgae-based CCU a significant contribution to global carbon mitigation solutions.

Nguyen, LT, Pollock, CA & Saad, S 2023, 'Nutrition and Developmental Origins of Kidney Disease', Nutrients, vol. 15, no. 19, pp. 4207-4207.
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The developmental programming hypothesis proposes that adverse environmental insults during critical developmental periods increase the risk of diseases later in life. The kidneys are deemed susceptible to such a process, although the exact mechanisms remain elusive. Many factors have been reported to contribute to the developmental origin of chronic kidney diseases (CKD), among which peri-gestational nutrition has a central role, affecting kidney development and metabolism. Physiologically, the link between malnutrition, reduced glomerular numbers, and increased blood pressure is key in the developmental programming of CKD. However, recent studies regarding oxidative stress, mitochondrial dysfunction, epigenetic modifications, and metabolic changes have revealed potential novel pathways for therapeutic intervention. This review will discuss the role of imbalanced nutrition in the development of CKD.

Nickovic, S, Petković, S, Ilić, L, Pejanović, G, Mijić, Z, Huete, A & Marks, G 2023, 'Prediction of airborne pollen and sub-pollen particles for thunderstorm asthma outbreaks assessment', Science of The Total Environment, vol. 864, pp. 160879-160879.
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Nie, X, Dong, K, Tian, Y, Zong, C, Chen, Z, Wang, X & Zhao, Y 2023, 'A green analysis detection of formaldehyde in grooming products by surface enhanced Raman spectroscopy', Materials Today Sustainability, vol. 22, pp. 100303-100303.
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Nielsen, DA & Petrou, K 2023, 'Lipid stores reveal the state of the coral-algae symbiosis at the single-cell level', ISME Communications, vol. 3, no. 1, p. 29.
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Abstract Coral reefs worldwide are threatened by environmental stress. The observable decline in coral cover, is principally due to the intensifying breakdown of the coral symbiosis, a process known as ‘bleaching’. Overproduction of reactive oxygen species (ROS) is considered a key driver of coral bleaching, where environmental stress leads to increased ROS expression. To explore the link between ROS damage and symbiont status, we measured lipid peroxidation (LPO), a ubiquitous form of ROS damage, in the lipid stores of individual endo- and ex-symbiotic algal cells of three coral species, using confocal microscopy and a lipid hydroperoxide sensitive fluorescent dye. We found LPO was higher in endosymbionts, while lipid volume was greater in ex-symbiotic cells. Cluster analysis revealed three metabolic profiles differentiating endosymbiotic (#1: high LPO, low lipid) and ex-symbiotic cells (#3: low LPO, high lipid), with the intermediate group (#2) containing both cell types. Heat stress caused endosymbionts of Pocillopora acuta to shift away from cluster #1, suggesting this cluster represents cells in healthy/stable symbiosis. Our study delivers a new means to assess the coral symbiosis, demonstrating that symbiont LPO ratio combined with lipid store volume is a robust metabolic marker for the state of the symbiosis at the cellular level.

Nielsen, S, Barratt, M, Hiley, S, Bartlett, M, Latimer, J, Jauncey, M, Roux, C, Morelato, M, Clark, N, Kowalski, M, Gilbert, M, Francia, L, Shipton, A, Gerostamoulos, D, Glowacki, L & Lam, T 2023, 'Monitoring for fentanyl within Australian supervised injecting facilities: Findings from feasibility testing of novel methods and collaborative workshops', International Journal of Drug Policy, vol. 115, pp. 104015-104015.
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Nonahal, M, Horder, J, Gale, A, Ding, L, Li, C, Hennessey, M, Ha, ST, Toth, M & Aharonovich, I 2023, 'Deterministic Fabrication of a Coupled Cavity–Emitter System in Hexagonal Boron Nitride', Nano Letters, vol. 23, no. 14, pp. 6645-6650.
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Nonahal, M, Li, C, Ren, H, Spencer, L, Kianinia, M, Toth, M & Aharonovich, I 2023, 'Engineering Quantum Nanophotonic Components from Hexagonal Boron Nitride', Laser & Photonics Reviews, vol. 17, no. 8.
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AbstractIntegrated quantum photonics (IQP) provides a path to practical, scalable quantum computation, communications and information processing. Realization of an IQP platform requires controlled engineering of many nanophotonic components. However, the range of materials for monolithic platforms is limited by the simultaneous need for high‐quality quantum light sources, high optical performance, and availability of scalable nanofabrication techniques. Here, the fabrication of IQP components from the recently emerged material hexagonal boron nitride (hBN), including tapered waveguides, microdisks, and 1D and 2D photonic crystal cavities, is demonstrated. Resonators with quality factors greater than 4000 are achieved, and proof‐of‐principle complex, free‐standing IQP circuitry fabricated from single‐crystal hBN is engineered. The results show the potential of hBN for scalable integrated quantum technologies.

Noorian, P, Hoque, MM, Espinoza-Vergara, G & McDougald, D 2023, 'Environmental Reservoirs of Pathogenic Vibrio spp. and Their Role in Disease: The List Keeps Expanding', pp. 99-126.
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O’Brien, L, Siboni, N, Seymour, JR, Balzer, M & Mitrovic, S 2023, 'Tributary Inflows to a Regulated River Influence Bacterial Communities and Increase Bacterial Carbon Assimilation', Microbial Ecology, vol. 86, no. 4, pp. 2642-2654.
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AbstractInflows from unregulated tributaries change the physical, chemical, and biotic conditions in receiving regulated rivers, impacting microbial community structure and metabolic function. Understanding how tributary inflows affect bacterial carbon production (BCP) is integral to understanding energy transfer in riverine ecosystems. To investigate the role of tributary inflows on bacterial community composition and BCP, a ~90th percentile natural flow event was sampled over 5 days along the Lachlan River and its tributaries within the Murray-Darling Basin of eastern Australia. Increased tributary inflows after rainfall corresponded with a significantly different and more diverse bacterial community in the regulated mainstem. The major contributor to this difference was an increase in relative abundance of bacterial groups with a potential metabolic preference for humic substances (Burkholderiaceae Polynucleobacter, Alcaligenaceae GKS98 freshwater group, Saccharimonadia) and a significant decrease in Spirosomaceae Pseudarcicella, known to metabolise algal exudates. Increases in orthophosphate and river discharge explained 31% of community change, suggesting a combination of resource delivery and microbial community coalescence as major drivers. BCP initially decreased significantly with tributary inflows, but the total load of carbon assimilated by bacteria increased by up to 20 times with flow due to increased water volume. The significant drivers of BCP were dissolved organic carbon, water temperature, and conductivity. Notably, BCP was not correlated with bacterial diversity or community composition. Tributary inflows were shown to alter mainstem bacterial community structure and metabolic function to take advantage of fresh terrestrial dissolved organic material, resulting in substantial changes to riverine carbon assimilation over sm...

O’Connell, MJ, Fowler, AM, Allan, SJ, Beretta, GA & Booth, DJ 2023, 'Subtropical coral expansion into SE Australia: a haven for both temperate and expatriating tropical reef fishes', Coral Reefs, vol. 42, no. 6, pp. 1257-1262.
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AbstractWe examined reef fish assemblages in and adjacent to a newly established coral bed (subtropical Pocillopora aliciae) in temperate south-eastern Australia, to understand whether novel coral habitat is facilitating assemblages of range-expanding tropical and local temperate fishes. This is the first comprehensive assessment of fish species associating with this novel coral habitat within a temperate environment. Twenty fish species were observed associating with the coral (8 tropical and 12 temperate). Both temperate and tropical species were observed at greater (up to 48 times higher) densities on the coral than on nearby temperate rocky reef in the area, suggesting that the corals generally concentrate fish and may aid in tropicalisation for species that use subtropical coral as habitat. Future research should investigate the ongoing expansion of this coral, the relative quality of coral habitat for fish in temperate regions and the potential implications for functioning of temperate rocky reef ecosystems.

Ochwada-Doyle, F, Hughes, J, Fowler, AM, Murphy, J, Stark, K, Lowry, M, West, L & Taylor, MD 2023, 'Quantifying the potential impact of reducing recreational harvest limits on the catch of a key marine species using off-site angler survey data', ICES Journal of Marine Science, vol. 80, no. 2, pp. 295-307.
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Abstract Recreational fishing can have substantial ecological impacts, which must be managed against a background of critical socio-economic factors. However, it is often difficult to assess the effect of altered management arrangements on this sector’s harvest. Recreational fishing surveys can assist in quantifying the impact of changes to harvest limits. Here, we use survey data collected in 2013/2014 and 2017/2018 to estimate the total catch of Dusky Flathead (Platycephalus fuscus), a key Australian marine species, under a daily harvest limit of 10 fish per angler and simulated scenarios where the limit is reduced to 5, 3, or 1 fish per angler. We then test the significance of these changes in harvest limit on catch and also model the potential effects of year and region using generalized linear mixed models (GLMMz). For both sampled time periods, the GLMMz found that only the most stringent harvest limit reduction to 1 fish per angler would lower retained harvest significantly. None of the reductions in harvest limit increased the number of released Dusky Flathead significantly. We discuss how this novel quantitative approach can be used to inform alternative output management regulations by taking into account their potential ecological and socio-economic benefits for a recreational fishery.

Oktar, FN, Unal, S, Gunduz, O, Nissan, BB, Macha, IJ, Akyol, S, Duta, L, Ekren, N, Altan, E & Yetmez, M 2023, 'Correction to: Marine-derived bioceramics for orthopedic, reconstructive and dental surgery applications', Journal of the Australian Ceramic Society, vol. 59, no. 1, pp. 267-267.
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Oktar, FN, Unal, S, Gunduz, O, Nissan, BB, Macha, IJ, Akyol, S, Duta, L, Ekren, N, Altan, E & Yetmez, M 2023, 'Marine-derived bioceramics for orthopedic, reconstructive and dental surgery applications', Journal of the Australian Ceramic Society, vol. 59, no. 1, pp. 57-81.
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Ortega, JS, Corrales-Orovio, R, Ralph, P, Egaña, JT & Gentile, C 2023, 'Photosynthetic microorganisms for the oxygenation of advanced 3D bioprinted tissues', Acta Biomaterialia, vol. 165, pp. 180-196.
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3D bioprinting technology has emerged as a tool that promises to revolutionize the biomedical field, including tissue engineering and regeneration. Despite major technological advancements, several challenges remain to be solved before 3D bioprinted tissues could be fully translated from the bench to the bedside. As oxygen plays a key role in aerobic metabolism, which allows energy production in the mitochondria; as a consequence, the lack of tissue oxygenation is one of the main limitations of current bioprinted tissues and organs. In order to improve tissue oxygenation, recent approaches have been established for a broad range of clinical applications, with some already applied using 3D bioprinting technologies. Among them, the incorporation of photosynthetic microorganisms, such as microalgae and cyanobacteria, is a promising approach that has been recently explored to generate chimerical plant-animal tissues where, upon light exposure, oxygen can be produced and released in a localized and controlled manner. This review will briefly summarize the state-of-the-art approaches to improve tissue oxygenation, as well as studies describing the use of photosynthetic microorganisms in 3D bioprinting technologies. STATEMENT OF SIGNIFICANCE: 3D bioprinting technology has emerged as a tool for the generation of viable and functional tissues for direct in vitro and in vivo applications, including disease modeling, drug discovery and regenerative medicine. Despite the latest advancements in this field, suboptimal oxygen delivery to cells before, during and after the bioprinting process limits their viability within 3D bioprinted tissues. This review article first highlights state-of-the-art approaches used to improve oxygen delivery in bioengineered tissues to overcome this challenge. Then, it focuses on the emerging roles played by photosynthetic organisms as novel biomaterials for bioink generation. Finally, it provides considerations around current challenges...

Osborne, B, Siboni, N, Seymour, JR, Ralph, P & Pernice, M 2023, 'Exploring the potential of algae-bacteria interactions in the biocontrol of the marine pathogen Vibrio parahaemolyticus', Journal of Applied Phycology, vol. 35, no. 6, pp. 2731-2743.
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AbstractThe marine bacterium Vibrio parahaemolyticus is the leading cause of seafood-related food poisoning worldwide and a pathogen of marine species harvested in aquaculture. An outbreak of pathogenic V. parahaemolyticus within crustacean and bi-valve aquaculture facilities often results in significant loss of farmed product and in the spread of the pathogen into the human population. Evidence shows several marine bacteria and microalgae species have antibacterial effects against marine pathogens, including V. parahaemolyticus. This study explored the potential of combining possible mutualistic species as a consortium to enhance antibacterial properties against V. parahaemolyticus. Marine bacteria and microalgae were screened with the aim of identifying those able to successfully coexist while demonstrating growth suppression of multiple V. parahaemolyticus strains. This trial involved four screening phases to find effective inhibitor species and to gain insight into species-specific influences on cell growth. The combination of Tetraselmis sp. and Pseudoalteromonas peptidolytica achieved the greatest inhibition rate of V. parahaemolyticus of all combinations. This pairing resulted in the significant reduction of up to 24 ± 15% in Vibrio sp. copy number mL−1 day−1 in two of the five examined V. parahaemolyticus strains within five days, compared to control cultures absent of probiotic bacteria. Applying probiotic consortia such as this has the potential for use as a biocontrol technique within mariculture, but it will require additional research into the self-sustainability of successful consortia in natural aqua...

Otsuka, Y, Ben-Nissan, B, Kono, H, Sasaki, T & Kikuchi, M 2023, 'Mechanochemical synthesis and characterization of strontium substituted apatite for biomedical application', Open Ceramics, vol. 16, pp. 100459-100459.
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Otsuka, Y, Sasaki, D, Kusamori, K, Nishikawa, M & Ben-Nissan, B 2023, 'Investigation of the crystallinity change after the addition of magnesium hydroxides into the calcium phosphate during mechanochemical synthesis: an FTIR spectroscopy, XRD analysis, chemometrics, and cell culture', Journal of the Australian Ceramic Society, vol. 59, no. 5, pp. 1373-1380.
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Pamphlett, R & Bishop, DP 2023, 'The toxic metal hypothesis for neurological disorders', Frontiers in Neurology, vol. 14, p. 1173779.
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Multiple sclerosis and the major sporadic neurogenerative disorders, amyotrophic lateral sclerosis, Parkinson disease, and Alzheimer disease are considered to have both genetic and environmental components. Advances have been made in finding genetic predispositions to these disorders, but it has been difficult to pin down environmental agents that trigger them. Environmental toxic metals have been implicated in neurological disorders, since human exposure to toxic metals is common from anthropogenic and natural sources, and toxic metals have damaging properties that are suspected to underlie many of these disorders. Questions remain, however, as to how toxic metals enter the nervous system, if one or combinations of metals are sufficient to precipitate disease, and how toxic metal exposure results in different patterns of neuronal and white matter loss. The hypothesis presented here is that damage to selective locus ceruleus neurons from toxic metals causes dysfunction of the blood–brain barrier. This allows circulating toxicants to enter astrocytes, from where they are transferred to, and damage, oligodendrocytes, and neurons. The type of neurological disorder that arises depends on (i) which locus ceruleus neurons are damaged, (ii) genetic variants that give rise to susceptibility to toxic metal uptake, cytotoxicity, or clearance, (iii) the age, frequency, and duration of toxicant exposure, and (iv) the uptake of various mixtures of toxic metals. Evidence supporting this hypothesis is presented, concentrating on studies that have examined the distribution of toxic metals in the human nervous system. Clinicopathological features shared between neurological disorders are listed that can be linked to toxic metals. Details are provided on how the hypothesis applies to multiple sclerosis and the major neurodegenerative disorders. Further avenues to explore the toxic metal hypothesis for neurological disorders are suggested. In conclusion, environme...

Pamphlett, R, Buckland, ME & Bishop, DP 2023, 'Potentially toxic elements in the brains of people with multiple sclerosis', Scientific Reports, vol. 13, no. 1, p. 655.
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AbstractPotentially toxic elements such as lead and aluminium have been proposed to play a role in the pathogenesis of multiple sclerosis (MS), since their neurotoxic mechanisms mimic many of the pathogenetic processes in MS. We therefore examined the distribution of several potentially toxic elements in the autopsied brains of people with and without MS, using two methods of elemental bio-imaging. Toxicants detected in the locus ceruleus were used as indicators of past exposures. Autometallography of paraffin sections from multiple brain regions of 21 MS patients and 109 controls detected inorganic mercury, silver, or bismuth in many locus ceruleus neurons of both groups, and in widespread blood vessels, oligodendrocytes, astrocytes, and neurons of four MS patients and one control. Laser ablation-inductively coupled plasma-mass spectrometry imaging of pons paraffin sections from all MS patients and 12 controls showed that combinations of iron, silver, lead, aluminium, mercury, nickel, and bismuth were present more often in the locus ceruleus of MS patients and were located predominantly in white matter tracts. Based on these results, we propose that metal toxicants in locus ceruleus neurons weaken the blood–brain barrier, enabling multiple interacting toxicants to pass through blood vessels and enter astrocytes and oligodendroglia, leading to demyelination.

Pan, Y, Peng, D, Chen, JM, Myneni, RB, Zhang, X, Huete, AR, Fu, YH, Zheng, S, Yan, K, Yu, L, Zhu, P, Shen, M, Ju, W, Zhu, W, Xie, Q, Huang, W, Chen, Z, Huang, J & Wu, C 2023, 'Climate-driven land surface phenology advance is overestimated due to ignoring land cover changes', Environmental Research Letters, vol. 18, no. 4, pp. 044045-044045.
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Abstract Global warming has led to earlier spring green-up dates (GUDs) in recent decades with significant consequences for global carbon and hydrologic cycles. In addition to changes in climate, land cover change (LCC), including interchanges between vegetation and non-vegetation, and among plants with different functional traits, may also affect GUD. Here, we analyzed how satellite-derived GUD from 1992 to 2020 was impacted by changes in temperature, precipitation, standardized precipitation evapotranspiration index (SPEI), solar radiation, and LCC for the Northern Hemisphere (>30° N). While the climate variables had larger impact overall, variability in GUD was controlled by LCC for 6% of the Northern Hemisphere, with systematically earlier or later changes among transitions between different land cover types. These changes were found mainly along the southeastern coast of the United States, in Central-north Europe, and across northeastern China. We further showed that climate change attribution of earlier GUD during 1992–2020 was overestimated by three days when the impact of LCC was ignored. Our results deepen the understanding of how LCC impacts GUD variability and enables scientists to more accurately evaluate the impact of climate change on land surface phenology.

Panthi, VK, Imran, M, Chaudhary, A, Paudel, KR & Mohammed, Y 2023, 'The significance of quercetin-loaded advanced nanoformulations for the management of diabetic wounds', Nanomedicine, vol. 18, no. 4, pp. 391-411.
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Quercetin is a well-known plant flavanol that exhibits multiple biological activities, including antioxidant, anti-inflammatory and anticancer activities. The role of quercetin in wound healing has been widely explored by a range of researchers in different models. However, the physicochemical properties, such as solubility and permeability, of this compound are low, which ultimately limits its bioavailability on the target site. To overcome these limitations for successful therapy, scientists have developed a range of nanoformulations that provide effective therapeutic potential. In this review, the broad mechanism of quercetin for acute and chronic wounds is covered. A compilation of recent advances on the horizon of wound healing via quercetin is incorporated with several advanced nanoformulations.

Patel, VK, Vishwas, S, Kumar, R, De Rubis, G, Shukla, SD, Paudel, KR, Manandhar, B, Singh, TG, Chellappan, DK, Gulati, M, Kaur, IP, Allam, VSRR, Hansbro, PM, Oliver, BG, MacLoughlin, R, Singh, SK & Dua, K 2023, 'Tackling the cytokine storm using advanced drug delivery in allergic airway disease', Journal of Drug Delivery Science and Technology, vol. 82, pp. 104366-104366.
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Paudel, KR, Rajput, R, De Rubis, G, Raju Allam, VSR, Williams, KA, Singh, SK, Gupta, G, Salunke, P, Hansbro, PM, Gerlach, J & Dua, K 2023, 'In vitro anti-cancer activity of a polyherbal preparation, VEDICINALS®9, against A549 human lung adenocarcinoma cells', Pathology - Research and Practice, vol. 250, pp. 154832-154832.
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Petrou, K 2023, 'Phytoplankton–Bacteria Interactions 1.0', Microorganisms, vol. 11, no. 5, pp. 1188-1188.
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Phytoplankton and bacteria regulate many essential functions in aquatic ecosystems [...]

Petrou, K 2023, 'Phytoplankton-Bacteria Interactions 2.0', Microorganisms, vol. 11, no. 6, pp. 1536-1536.
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There are multiple ways in which phytoplankton and bacteria interact, starting from the fundamental symbiotic associations of direct attachment, through intimate interactions within the phytoplankton phycosphere, to random associations within the water column via the exudation and cycling of dissolved organic carbon (DOC) and other chemical compounds [...]

Pitiyarachchi, O, Lee, YC, Sim, H-W, Srirangan, S, Mapagu, C, Kirk, J, Harnett, PR, Balleine, RL, Bowtell, DDL, Samimi, G, Brand, AH, Marsh, DJ, Beale, P, Anderson, L, Bouantoun, N, Provan, P, Ramus, SJ, DeFazio, A & Friedlander, M 2023, 'Older age should not be a barrier to testing for somatic variants in homologous recombination DNA repair-related genes in patients with high-grade serous ovarian carcinoma', Translational Oncology, vol. 31, pp. 101638-101638.
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BACKGROUND: Somatic pathogenic variants (PVs) in homologous recombination DNA repair (HR)-related genes found in high-grade serous ovarian carcinomas (HGSC) are not well-characterised in older patients (≥70 years). This may reflect low testing rates in older patients. METHODS: Data from 1210 HGSC patients in AACR Project GENIE and 324 patients in an independent dataset INOVATe were analysed. Cases where somatic variants could be distinguished from germline variants were included, and analysis was restricted to those with a somatic TP53 variant, to ensure cases were HGSC. RESULTS: Of 1210 patients in GENIE, 27% (n = 325) were aged ≥70 years at testing. Patients with somatic-only PVs in BRCA2 were older compared with BRCA1 (median 71 vs 60 years, p = 0.002). Median age for 21 patients with somatic-only PVs in 11 other HR-related genes ranged from 40 to 67 years. In older patients, 7% (n = 22) had somatic BRCA1/2 PVs, and 1% (n = 2) had PVs other HR-related genes; this rate was not significantly different to younger patients (<70 years), 7% (n = 62) BRCA1/2 and 2% (n = 19) other HR-related genes (p = 0.36). The overall frequency of somatic BRCA1/2 PVs was similar in INOVATe (n = 25; 7.7%) and somatic-only BRCA2 PVs were again found in older patients compared with BRCA1 (median age: at testing, 70 vs 63 years; at diagnosis, 68 vs 60 years). CONCLUSIONS: The overall frequency of somatic-only PVs in HR-related genes was similar in older and younger patients with HGSC, highlighting the importance of somatic testing irrespective of age. Limiting somatic testing by age may exclude patients who could benefit from maintenance poly(ADP-ribose) polymerase (PARP) inhibitors.

Piwczyński, M, Granjon, L, Trzeciak, P, Carlos Brito, J, Oana Popa, M, Daba Dinka, M, Johnston, NP & Boratyński, Z 2023, 'Unraveling phylogenetic relationships and species boundaries in the arid adapted Gerbillus rodents (Muridae: Gerbillinae) by RAD-seq data', Molecular Phylogenetics and Evolution, vol. 189, pp. 107913-107913.
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Pokhrel, A, Dinh, H, Li, L, Hassan, KA, Cain, AK & Paulsen, IT 2023, 'Identification of a Novel LysR Family Transcriptional Regulator Controlling Acquisition of Sulfur Sources in <i>Acinetobacter baumannii</i>', Microbial Physiology, vol. 33, no. 1, pp. 27-35.
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<sc>l</sc>-cysteine biosynthesis from inorganic sulfur represents a major mechanism by which reduced sulfur is incorporated into organic compounds. Cysteine biosynthesis and regulation is well characterized in <i>Escherichia coli</i>. However, the regulation of sulfur metabolism in <i>Acinetobacter baumannii</i> is only partly understood, with the LysR-type regulator, GigC known to control some aspects of sulfur reduction. In this study, we have used transcriptomics and bioinformatic analyses to characterize a novel LysR-type transcriptional regulator encoded by ABUW_1016 (<i>cbl</i>), in a highly multidrug resistant and virulent isolate of <i>A. baumannii.</i> We have shown that Cbl is involved in controlling expression of the genes required for uptake and reduction of various sulfur sources in <i>A. baumannii</i>. Collectively, we have identified the global regulon of Cbl and proposed a model of cysteine biosynthesis and its regulation by Cbl and GigC in <i>A. baumannii</i>.

Poulton, CG, Zeisberger, M & Schmidt, MA 2023, 'Coupled waveguide model for computing phase and transmission through nanopillar-based metasurfaces', Optics Express, vol. 31, no. 26, pp. 44551-44551.
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Dielectric metasurfaces are important in modern photonics due to their unique beam shaping capabilities. However, the standard tools for the computation of the phase and transmission through a nanopillar-based metasurface are either simple, approximating the properties of the surface by that of a single cylinder, or use full 3D numerical simulations. Here we introduce a new analytical model for computing metasurface properties which explicitly takes into account the effect of the lattice geometry. As an example we investigate silicon nanopillar-based metasurfaces, examining how the transmission properties depend on the presence of different modes in the unit cell of the metasurface array. We find that the new model outperforms the isolated cylinder model in predicting the phase, and gives excellent agreement with full numerical simulations when the fill fraction is moderate. Our model offers a waveguide perspective for comprehending metasurface properties, linking it to fiber optics and serving as a practical tool for future metasurface design.

Pouwels, SD, van den Berge, M, Vasse, GF, Timens, W, Brandsma, C-A, Aliee, H, Hiemstra, PS, Guryev, V & Faiz, A 2023, 'Smoking increases expression of the SARS-CoV-2 spike protein-binding long ACE2 isoform in bronchial epithelium', Respiratory Research, vol. 24, no. 1, p. 130.
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AbstractAfter more than two years the COVID-19 pandemic, that is caused by infection with the respiratory SARS-CoV-2 virus, is still ongoing. The risk to develop severe COVID-19 upon SARS-CoV-2 infection is increased in individuals with a high age, high body mass index, and who are smoking. The SARS-CoV-2 virus infects cells of the upper respiratory tract by entering these cells upon binding to the Angiotensin-converting enzyme 2 (ACE2) receptor. ACE2 is expressed in various cell types in the lung but the expression is especially high in goblet and ciliated cells. Recently, it was shown that next to its full-length isoform, ACE2 also has a short isoform. The short isoform is unable to bind SARS-CoV-2 and does not facilitate viral entry. In the current study we investigated whether active cigarette smoking increases the expression of the long or the short ACE2 isoform. We showed that in active smokers the expression of the long, active isoform, but not the short isoform of ACE2 is higher compared to never smokers. Additionally, it was shown that the expression of especially the long, active isoform of ACE2 was associated with secretory, club and goblet epithelial cells. This study increases our understanding of why current smokers are more susceptible to SARS-CoV-2 infection, in addition to the already established increased risk to develop severe COVID-19.

Power, T, Kennedy, P, Chen, H, Martinez-Maldonado, R, McGregor, C, Johnson, A, Townsend, L & Hayes, C 2023, 'Learning to Manage De-escalation Through Simulation: An Exploratory Study', Clinical Simulation in Nursing, vol. 77, pp. 23-29.
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Pravadali-Cekic, S, Vojvodic, A, Violi, JP, Mitrovic, SM, Rodgers, KJ & Bishop, DP 2023, 'Simultaneous Analysis of Cyanotoxins β-N-methylamino-L-alanine (BMAA) and Microcystins-RR, -LR, and -YR Using Liquid Chromatography–Tandem Mass Spectrometry (LC-MS/MS)', Molecules, vol. 28, no. 18, pp. 6733-6733.
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β-N-methylamino-L-alanine (BMAA) and its isomers, 2,4-diaminobutyric acid (2,4-DAB) and N-(2-aminoethyl)-glycine (AEG), along with microcystins (MCs)-RR, -LR, and -YR (the major MC congeners), are cyanotoxins that can cause detrimental health and environmental impacts during toxic blooms. Currently, there are no reverse-phase (RP) LC-MS/MS methods for the simultaneous detection and quantification of BMAA, its isomers, and the major MCs in a single analysis; therefore, multiple analyses are required to assess the toxic load of a sample. Here, we present a newly developed and validated method for the detection and quantification of BMAA, 2,4-DAB, AEG, MC-LR, MC-RR, and MC-YR using RP LC-MS/MS. Method validation was performed, assessing linearity (r2 > 0.996), accuracy (>90% recovery for spiked samples), precision (7% relative standard deviation), and limits of detection (LODs) and quantification (LOQs) (ranging from 0.13 to 1.38 ng mL−1). The application of this combined cyanotoxin analysis on a culture of Microcystis aeruginosa resulted in the simultaneous detection of 2,4-DAB (0.249 ng mg−1 dry weight (DW)) and MC-YR (4828 ng mg−1 DW). This study provides a unified method for the quantitative analysis of BMAA, its isomers, and three MC congeners in natural environmental samples.

Price, OF, Mikac, K, Wilson, N, Roberts, B, Critescu, RH, Gallagher, R, Mallee, J, Donatiou, P, Webb, J, Keith, DA, Letnic, M & Mackenzie, BDE 2023, 'Short‐term impacts of the 2019–20 fire season on biodiversity in eastern Australia', Austral Ecology, vol. 48, no. 1, pp. 3-11.
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AbstractTo address uncertainties surrounding the impacts of unprecedented 2019–20 bushfires in south‐eastern Australia, we convened a symposium on field‐measured impacts on biodiversity for the 2020 Ecological Society of Australia conference. Nine presentations covered a range of studies on plant species and communities, and reptiles and mammals. Here, we summarize the presentations and review other field studies from NSW, some of which are currently unpublished. The impacts were extensive, but results also estimated survival rate perhaps higher than first reported in the media. More than half of individual mammal, reptile and threatened rainforest trees may have survived the fire, though small populations remain very vulnerable to second fire in the near future. Comprehensive understanding of the impacts of these fires requires much more field study, and for the results to be interpreted in the context of the broader fire regime. The symposium was an important early step in that understanding.

Price, S, Kuzhiumparambil, U, Pernice, M, Herdean, A & Ralph, P 2023, 'Enhancement of cyanobacterial PHB production using random chemical mutagenesis with detection through FACS', Bioprocess and Biosystems Engineering, vol. 46, no. 2, pp. 297-306.
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Prity, FT, Tobin, LA, Maharajan, R, Paulsen, IT, Cain, AK & Hamidian, M 2023, 'The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate', Microbial Genomics, vol. 9, no. 5, p. mgen001010.
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Acinetobacter baumannii is an important opportunistic pathogen known for its high levels of resistance to many antibiotics, particularly those considered last resorts such as colistin and carbapenems. Plasmids of this organism are increasingly associated with the spread of clinically important antibiotic resistance genes. Although A. baumannii is a ubiquitous organism, to date, most of the focus has been on studying strains recovered from clinical samples ignoring those isolated in the environment (soil, water, food, etc.). Here, we analysed the genetic structures of eight novel plasmids carried by an environmental colistin-resistant A. baumannii (strain E-072658) recovered in a recycled fibre pulp in a paper mill in Finland. It was shown that E-072658 carries a new variant of the mcr-4 colistin resistance gene (mcr-4.7) in a novel Tn3-family transposon (c...

Qiao, L, Fang, L, Lv, Q, Xu, S, Jia, F, Wu, W, Picozzi, S, Pyatakov, AP, Reimers, JR & Ren, W 2023, 'Predicting layered itinerant magnetic Fe3SiSe2 with spontaneous valley polarization', Journal of Applied Physics, vol. 133, no. 20.
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Density functional theory calculations are performed to systematically investigate the electronic and magnetic properties of few-layer and bulk Fe3SiSe2 (FSS). We predict that the bulk FSS has a metallic ground state and a layered structure displaying intralayer ferromagnetic ordering and interlayer antiferromagnetic ordering. The itinerant magnetism in the FSS was determined by the Stoner criterion. Predictions of the absence of unstable phonon modes and a moderate cleavage energy of only 28.3 meV/Å2 suggest the possibility of stabilizing FSS in a monolayer form. The calculated spin–orbit coupling facilitates not only a large magnetocrystalline anisotropy energy, around 500 μeV/Fe, but also spontaneous valley polarization in odd-numbered layer systems. These systems have net magnetic moments as the magnetic moments of AFM-ordered layers are not fully compensated in the odd-numbered layer case and are predicted to show 2D metallic behaviors. The magnitude of the valley polarization in odd-numbered layered systems decreases from 18 meV with layer number but is absent in even-layered structures, thus showing an odd–even oscillation effect. Experimental realization of this bidimensional metallic magnet is, therefore, expected to widen the arena of two-dimensional materials that show exotic phenomena.

Qu, J, Cao, X, Gao, L, Li, J, Li, L, Xie, Y, Zhao, Y, Zhang, J, Wu, M & Liu, H 2023, 'Electrochemical Carbon Dioxide Reduction to Ethylene: From Mechanistic Understanding to Catalyst Surface Engineering', Nano-Micro Letters, vol. 15, no. 1.
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AbstractElectrochemical carbon dioxide reduction reaction (CO2RR) provides a promising way to convert CO2 to chemicals. The multicarbon (C2+) products, especially ethylene, are of great interest due to their versatile industrial applications. However, selectively reducing CO2 to ethylene is still challenging as the additional energy required for the C–C coupling step results in large overpotential and many competing products. Nonetheless, mechanistic understanding of the key steps and preferred reaction pathways/conditions, as well as rational design of novel catalysts for ethylene production have been regarded as promising approaches to achieving the highly efficient and selective CO2RR. In this review, we first illustrate the key steps for CO2RR to ethylene (e.g., CO2 adsorption/activation, formation of *CO intermediate, C–C coupling step), offering mechanistic understanding of CO2RR conversion to ethylene. Then the alternative reaction pathways and conditions for the formation of ethylene and competitive products (C1 and other C2+ products) are investigated, guiding the further design and development of preferred conditions for ethylene generation. Engineering strategies of Cu-based catalysts for CO2RR-ethylene are further summarized, and the correlations of reaction mechanism/pathways, engineering strategies and selectivity are elaborated. Finally, major challenges and perspectives in the research area of CO2RR are proposed for future development and practical applications.

Quigley, KM, Alvarez-Roa, C, Raina, J-B, Pernice, M & van Oppen, MJH 2023, 'Heat-evolved microalgal symbionts increase thermal bleaching tolerance of coral juveniles without a trade-off against growth', Coral Reefs, vol. 42, no. 6, pp. 1227-1232.
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AbstractGlobal climate change is threatening the persistence of coral reefs as associated summer heatwaves trigger the loss of microalgal endosymbionts (Symbiodiniaceae) from the coral tissues, or coral bleaching. We infected aposymbiotic juveniles of the coral Acropora tenuis with either wildtype (WT10) or heat-evolved (SS1 or SS8) Symbiodiniaceae strains Cladocopium proliferum (formerly referred to as Cladocopium goreaui and Cladocopium C1acro). After 10 months at 27 °C, SS8-juveniles were 2 × larger than SS1- or WT10-juveniles. In response to a simulated heatwave (31 °C for 41 days), the WT10-juveniles bleached and showed a decline in respiration while cell densities and respiration in both SS-juvenile groups remained unchanged compared to the controls. These results reveal that some heat-evolved strains can increase the bleaching tolerance of juvenile corals without a trade-off against growth. This response is opposite to the lower nutrient provisioning often reported for naturally thermotolerant Symbiodiniaceae (e.g. genus Durusdinium), thereby offering enhanced fitness to the host without the ecological consequences of diminished growth.

Quintana Vigiola, G, Donnelly, S & Wan, K 2023, 'Housing Provision for Women Experiencing Domestic and Family Violence in NSW during COVID-19', Urban Policy and Research, vol. 41, no. 1, pp. 55-69.
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Quinteros, SL, von Krusenstiern, E, Snyder, NW, Tanaka, A, O’Brien, B & Donnelly, S 2023, 'The helminth derived peptide FhHDM-1 redirects macrophage metabolism towards glutaminolysis to regulate the pro-inflammatory response', Frontiers in Immunology, vol. 14, p. 1018076.
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We have previously identified an immune modulating peptide, termed FhHDM-1, within the secretions of the liver fluke, Fasciola hepatica, which is sufficiently potent to prevent the progression of type 1 diabetes and multiple sclerosis in murine models of disease. Here, we have determined that the FhHDM-1 peptide regulates inflammation by reprogramming macrophage metabolism. Specifically, FhHDM-1 switched macrophage metabolism to a dependence on oxidative phosphorylation fuelled by fatty acids and supported by the induction of glutaminolysis. The catabolism of glutamine also resulted in an accumulation of alpha ketoglutarate (α-KG). These changes in metabolic activity were associated with a concomitant reduction in glycolytic flux, and the subsequent decrease in TNF and IL-6 production at the protein level. Interestingly, FhHDM-1 treated macrophages did not express the characteristic genes of an M2 phenotype, thereby indicating the specific regulation of inflammation, as opposed to the induction of an anti-inflammatory phenotype per se. Use of an inactive derivative of FhHDM-1, which did not modulate macrophage responses, revealed that the regulation of immune responses was dependent on the ability of FhHDM-1 to modulate lysosomal pH. These results identify a novel functional association between the lysosome and mitochondrial metabolism in macrophages, and further highlight the significant therapeutic potential of FhHDM-1 to prevent inflammation.

Quiroz, M, Nott, DJ & Kohn, R 2023, 'Gaussian Variational Approximations for High-dimensional State Space Models', Bayesian Analysis, vol. 18, no. 3.
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Radfar, P, Ding, L, de la Fuente, LR, Aboulkheyr, H, Gallego-Ortega, D & Warkiani, ME 2023, 'Rapid metabolomic screening of cancer cells via high-throughput static droplet microfluidics', Biosensors and Bioelectronics, vol. 223, pp. 114966-114966.
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Effective isolation and in-depth analysis of Circulating Tumour Cells (CTCs) are greatly needed in diagnosis, prognosis and monitoring of the therapeutic response of cancer patients but have not been completely fulfilled by conventional approaches. The rarity of CTCs and the lack of reliable biomarkers to distinguish them from peripheral blood cells have remained outstanding challenges for their clinical implementation. Herein, we developed a high throughput Static Droplet Microfluidic (SDM) device with 38,400 chambers, capable of isolating and classifying the number of metabolically active CTCs in peripheral blood at single-cell resolution. Owing to the miniaturisation and compartmentalisation capability of our device, we first demonstrated the ability to precisely measure the lactate production of different types of cancer cells inside 125 pL droplets at single-cell resolution. Furthermore, we compared the metabolomic activity of leukocytes from healthy donors to cancer cells and showed the ability to differentiate them. To further prove the clinical relevance, we spiked cancer cell lines in human healthy blood and showed the possibility to detect the cancer cells from leukocytes. Lastly, we tested the workflow on 8 preclinical mammary mouse models including syngeneic 67NR (non-metastatic) and 4T1.2 (metastatic) models with Triple-Negative Breast Cancer (TNBC) as well as transgenic mouses (12-week-old MMTV-PyMT). The results have shown the ability to precisely distinguish metabolically active CTCs from the blood using the proposed SDM device. The workflow is simple and robust which can eliminate the need for specialised equipment and expertise required for single-cell analysis of CTCs and facilitate on-site metabolic screening of cancer cells.

Radfar, P, Ding, L, Es, HA & Warkiani, ME 2023, 'A Microfluidic Approach for Enrichment and Single-Cell Characterization of Circulating Tumor Cells from Peripheral Blood', pp. 141-150.
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Rahman, MA, Mamun, SMN, Hossain, AKMA & Ton-That, C 2023, 'ZnO Nanorods on Li-Doped ZnO Thin Films for Efficient p–n Homojunction Light-Emitting Diodes', ACS Applied Nano Materials, vol. 6, no. 17, pp. 15757-15763.
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Rangel Pinagé, E, Bell, DM, Longo, M, Silva, CA, Csillik, O & Huete, A 2023, 'Surface Energy Dynamics and Canopy Structural Properties in Intact and Disturbed Forests in the Southern Amazon', Journal of Geophysical Research: Biogeosciences, vol. 128, no. 9.
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AbstractThe Brazilian Amazon has been a focus of land development with large swaths of forests converted to agriculture. Forest degradation by selective logging and fires has accompanied the agricultural frontier and has resulted in significant impacts on Amazonian ecosystems. Changes in forest structure resulting from forest disturbances have large impacts on the surface energy balance, including on land surface temperature (LST) and evapotranspiration (ET). This study's objective is to assess the effects of forest disturbances on water fluxes and forest structure in a transitional forest site in the Southern Amazon. We used ET and LST products from MODIS and Landsat 8 and GEDI‐derived forest structure data to address our research questions. We found that disturbances induced seasonal water stress, more pronounced in croplands/pastures than in forests (differences up to 20% in the dry season), and more pronounced in second‐growth and recently burned areas than in logged and intact forests (differences up to 12% in the dry season). Moreover, ET and LST were negatively related, with more consistent relationships across disturbance classes in the dry season (R2: 0.41–0.87) than in the wet season (R2: 0.18–0.49). Forest and cropland or pasture classes showed contrasting relationships in the dry season. Finally, we found that forest structure exhibited stronger relationships with ET and LST in the most disturbed forests (R2: 0.01–0.43) than in the least disturbed forests (R2 < 0.05). Our findings help to elucidate degraded forests functioning under a changing climate and to improve estimates of water and energy fluxes in Amazonian degraded forests.

Rangsrikitphoti, P, Marquez-Garban, DC, Pietras, RJ, McGowan, E & Boonyaratanakornkit, V 2023, 'Sex steroid hormones and DNA repair regulation: Implications on cancer treatment responses', The Journal of Steroid Biochemistry and Molecular Biology, vol. 227, pp. 106230-106230.
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Rathnayake, SNH, Ditz, B, van Nijnatten, J, Sadaf, T, Hansbro, PM, Brandsma, CA, Timens, W, van Schadewijk, A, Hiemstra, PS, ten Hacken, NHT, Oliver, B, Kerstjens, HAM, van den Berge, M & Faiz, A 2023, 'Smoking induces shifts in cellular composition and transcriptome within the bronchial mucus barrier', Respirology, vol. 28, no. 2, pp. 132-142.
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AbstractBackground and ObjectiveSmoking disturbs the bronchial‐mucus‐barrier. This study assesses the cellular composition and gene expression shifts of the bronchial‐mucus‐barrier with smoking to understand the mechanism of mucosal damage by cigarette smoke exposure. We explore whether single‐cell‐RNA‐sequencing (scRNA‐seq) based cellular deconvolution (CD) can predict cell‐type composition in RNA‐seq data.MethodsRNA‐seq data of bronchial biopsies from three cohorts were analysed using CD. The cohorts included 56 participants with chronic obstructive pulmonary disease [COPD] (38 smokers; 18 ex‐smokers), 77 participants without COPD (40 never‐smokers; 37 smokers) and 16 participants who stopped smoking for 1 year (11 COPD and 5 non‐COPD‐smokers). Differential gene expression was used to investigate gene expression shifts. The CD‐derived goblet cell ratios were validated by correlating with staining‐derived goblet cell ratios from the COPD cohort. Statistics were done in the R software (false discovery rate p‐value < 0.05).ResultsBoth CD methods indicate a shift in bronchial‐mucus‐barrier cell composition towards goblet cells in COPD and non‐COPD‐smokers compared to ex‐ and never‐smokers. It shows that the effect was reversible within a year of smoking cessation. A reduction of ciliated and basal cells was observed with current smoking, which resolved following smoking cessation. The expression of mucin and sodium channel (ENaC) genes, but not chloride channel genes, were altered in COPD and current smokers compared to never smokers or ex‐smokers. The goblet cell‐derived staining scores correlate with CD‐derived goblet cell ratios.ConclusionSmoking alters bronchial‐mucus‐b...

Rathnayake, SNH, Ditz, B, Willemse, BWM, Timens, W, Kooistra, W, Heijink, IH, Oliver, BGG, van den Berge, M, Faiz, A, Aliee, H, Theis, FJ & Nawijn, MC 2023, 'Longitudinal Effects of 1-Year Smoking Cessation on Human Bronchial Epithelial Transcriptome', CHEST, vol. 164, no. 1, pp. 85-89.
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Rayamajhee, B, Williams, NLR, Siboni, N, Rodgers, K, Willcox, M, Henriquez, FL, Seymour, JR, Potts, J, Johnson, C, Scanes, P & Carnt, N 2023, 'Identification and quantification of Acanthamoeba spp. within seawater at four coastal lagoons on the east coast of Australia', Science of The Total Environment, vol. 901, pp. 165862-165862.
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Razavi Bazaz, S, Zhand, S, Salomon, R, Beheshti, EH, Jin, D & Warkiani, ME 2023, 'ImmunoInertial microfluidics: A novel strategy for isolation of small EV subpopulations', Applied Materials Today, vol. 30, pp. 101730-101730.
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Cancer-specific small extracellular vesicles (sEVs), known as exosomes, have shown a great promise to serve as novel biomarkers for cancer diagnosis and prognosis in liquid biopsies. However, the high heterogeneity of sEVs posed great technical challenges to acquiring their molecular information. A simple and reproducible method for isolating subpopulations of sEVs can significantly enhance the detection and stratification of these circulating biomarkers and their function. This study used the synergic effects of the immunoaffinity-based approach and inertial microfluidics (ImmunoInertial microfluidics) to isolate specific subpopulations of sEVs. At first, the cancer cell-derived sEVs were captured on microbeads of varying sizes which were functionalized with specific capture antibodies such as epithelial cell adhesion molecule (EpCAM), epidermal growth factor receptor (EGFR), and the programmed death-ligand 1 (PD-L1), facilitating the selective capture of sEVs. The sEVs-bearing microbeads were subsequently introduced to a series of inertial microfluidic channels, called iZExoSub (inertial zigzag microfluidics for exosome subpopulation separation), for size-based bead separation. Results revealed more than 90% efficiency in sEVs subpopulation separation, further proved via flow cytometry analysis data. Our approach is capable of selective isolation and quantitative detection of important biomarkers from sEVs subpopulations with high sensitivity and low cost and has the capacity to process samples of varying volumes, ranging from µL up to mL continuously. This system can outperform FACS machines in terms of sample throughput by orders of magnitudes. In addition, this study emphasized the necessity of using a consistent sEV marker (as capture and detector) across different samples for accurate assessment of subpopulations.

Rebej, M, Juřena, T, Vondál, J, Fuente Herraiz, D, Červený, J & Jegla, Z 2023, 'Numerical simulations and validation of single- and two-phase flow in a stirred lab-scale photobioreactor', Biosystems Engineering, vol. 230, pp. 35-50.
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Reddy, KD & Oliver, BGG 2023, 'Sexual dimorphism in chronic respiratory diseases', Cell & Bioscience, vol. 13, no. 1, p. 47.
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AbstractSex differences in susceptibility, severity, and progression are prevalent for various diseases in multiple organ systems. This phenomenon is particularly apparent in respiratory diseases. Asthma demonstrates an age-dependent pattern of sexual dimorphism. However, marked differences between males and females exist in other pervasive conditions such as chronic obstructive pulmonary disease (COPD) and lung cancer. The sex hormones estrogen and testosterone are commonly considered the primary factors causing sexual dimorphism in disease. However, how they contribute to differences in disease onset between males and females remains undefined. The sex chromosomes are an under-investigated fundamental form of sexual dimorphism. Recent studies highlight key X and Y-chromosome-linked genes that regulate vital cell processes and can contribute to disease-relevant mechanisms. This review summarises patterns of sex differences in asthma, COPD and lung cancer, highlighting physiological mechanisms causing the observed dimorphism. We also describe the role of the sex hormones and present candidate genes on the sex chromosomes as potential factors contributing to sexual dimorphism in disease.

Reich, HG, Camp, EF, Roger, LM & Putnam, HM 2023, 'The trace metal economy of the coral holobiont: supplies, demands and exchanges', Biological Reviews, vol. 98, no. 2, pp. 623-642.
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ABSTRACTThe juxtaposition of highly productive coral reef ecosystems in oligotrophic waters has spurred substantial interest and progress in our understanding of macronutrient uptake, exchange, and recycling among coral holobiont partners (host coral, dinoflagellate endosymbiont, endolithic algae, fungi, viruses, bacterial communities). By contrast, the contribution of trace metals to the physiological performance of the coral holobiont and, in turn, the functional ecology of reef‐building corals remains unclear. The coral holobiont's trace metal economy is a network of supply, demand, and exchanges upheld by cross‐kingdom symbiotic partnerships. Each partner has unique trace metal requirements that are central to their biochemical functions and the metabolic stability of the holobiont. Organismal homeostasis and the exchanges among partners determine the ability of the coral holobiont to adjust to fluctuating trace metal supplies in heterogeneous reef environments. This review details the requirements for trace metals in core biological processes and describes how metal exchanges among holobiont partners are key to sustaining complex nutritional symbioses in oligotrophic environments. Specifically, we discuss how trace metals contribute to partner compatibility, ability to cope with stress, and thereby to organismal fitness and distribution. Beyond holobiont trace metal cycling, we outline how the dynamic nature of the availability of environmental trace metal supplies can be influenced by a variability of abiotic factors (e.g. temperature, light, pH, etc.). Climate change will have profound consequences on the availability of trace metals and further intensify the myriad stressors that influence coral survival. Lastly, we suggest future research directions necessary for understanding the impacts of trace metals on the coral holobiont symbioses spanning subcellular to organismal levels, which will inform nutrient cyclin...

Reimers, JR & Low, PJ 2023, 'Molecular electronics: an Australian perspective', Australian Journal of Chemistry, vol. 76, no. 9, pp. 559-580.
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Molecular electronics is a scientific endeavour that, for 60 years, has offered the promise of new technologies in which molecules integrate with, if not entirely replace, semiconductor electronics. En route to the attainment of these ambitious goals, central aspects underpinning the pursuit of this science have proven critical to the development of related technologies, including organic photovoltaics (OPV) and organic light-emitting diodes (OLEDs). Looking ahead, new opportunities in the field abound, from the study of molecular charge transport and the elucidation of molecular reaction mechanisms, to the development of biocompatible and degradable electronics, and the construction of novel chemical sensors with exquisite sensitivity and specificity. This article reviews historical developments in molecular electronics, with a particular focus on Australia’s contributions to the area. Australia’s current activity in molecular electronics research is also summarised, highlighting the capacity to both advance fundamental knowledge and develop new technologies. Scientific aspects considered include capabilities in: single molecule and molecular–monolayer junction measurement; spectroscopic analysis of molecular components and materials; synthetic chemistry; computational analysis of molecular materials and junctions; and the development of theoretical concepts that describe the electrical characteristics of molecular components, materials and putative device structures. Technological aspects considered include various aspects of molecular material design and implementation, such as: OPV and OLED construction, sensing technologies and applications, and power generation from heat gradients or friction. Missing capabilities are identified, and a future pathway for Australian scientific and technological development envisaged.

Rennie, C, Huang, Y, Siwakoti, P, Du, Z, Padula, M, Bao, G, Tuch, BE, Xu, X & McClements, L 2023, 'In vitroevaluation of a hybrid drug-delivery nanosystem for fibrosis prevention in cell therapy for Type 1 diabetes', Nanomedicine, vol. 18, no. 1, pp. 53-66.
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Background: Implantation of insulin-secreting cells has been trialed as a treatment for Type 1 diabetes mellitus; however, the host immunogenic response limits their effectiveness. Methodology: The authors developed a core-shell nanostructure of upconversion nanoparticle-mesoporous silica for controlled local delivery of an immunomodulatory agent, MCC950, using near-infrared light and validated it in in vitro models of fibrosis. Results: The individual components of the nanosystem did not affect the proliferation of insulin-secreting cells, unlike fibroblast proliferation (p < 0.01). The nanosystem is effective at releasing MCC950 and preventing fibroblast differentiation (p < 0.01), inflammation (IL-6 expression; p < 0.05) and monocyte adhesion (p < 0.01). Conclusion: This MCC950-loaded nanomedicine system could be used in the future together with insulin-secreting cell implants to increase their longevity as a curative treatment for Type 1 diabetes mellitus.

Richards, C, Rad, DM, Zhand, S, Warkiani, M & McClements, L 2023, 'Evaluating gene delivery technologies to investigate the role of FKBPL in trophoblast function and the therapeutic potential of mesenchymal stem cell-derived extracellular vesicles', Placenta, vol. 140, pp. e48-e49.
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Robertson, IO, Scholten, SC, Singh, P, Healey, AJ, Meneses, F, Reineck, P, Abe, H, Ohshima, T, Kianinia, M, Aharonovich, I & Tetienne, J-P 2023, 'Detection of Paramagnetic Spins with an Ultrathin van der Waals Quantum Sensor', ACS Nano, vol. 17, no. 14, pp. 13408-13417.
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Rodrigues, JS, Kovács, L, Lukeš, M, Höper, R, Steuer, R, Červený, J, Lindberg, P & Zavřel, T 2023, 'Characterizing isoprene production in cyanobacteria – Insights into the effects of light, temperature, and isoprene on Synechocystis sp. PCC 6803', Bioresource Technology, vol. 380, pp. 129068-129068.
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Ross, P, Scanes, E, Byrne, M, Ainsworth, T, Donelson, J, Foo, S, Hutchings, P, Thiyagarajan, V & Parker, L 2023, 'Surviving the Anthropocene: The Resilience of Marine Animals to Climate Change', Oceanography and Marine Biology.

Ross, PM, Scanes, E & Locke, W 2023, 'Stress adaptation and resilience of academics in higher education', Asia Pacific Education Review.
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AbstractAcademics in higher education around the world indicate high levels of stress from multiple sources. The COVID-19 pandemic has only served to intensify stress levels. Adaptation and resilience are needed if academics, particularly those focused on education and teaching, are to endure, learn, andbounce backduring this era of stress and contribute to education quality and student learning. This review is organized to answer two key questions. First, what are the main forms of stress for academics, especially those focused on education and teaching? Second, what are the responses of academics to stress and is the concept of resilience relevant to understand the consequences for academic careers oriented toward education and education quality? To answer these questions, we first critically review the literature on the responses of academics to stress and the concept of resilience, which has been employed by multiple disciplines, including teacher education. We then broadly define the resilience of academics as their capacity to learn from and adapt to stress; our definition is perhaps less about individual personality characteristics and more associated with the relational aspect of the socioecological higher education ecosystem. There are, however, limits to resilience and its potential effects on education quality and student learning. Given higher education’s adverse operating environment and the significant contributions of academics to the knowledge economy and graduate quality, understanding and building the resilience of academics to adapt and succeed has never been more critical.

Rottet, S, Iqbal, S, Xifaras, R, Singer, MT, Scott, C, Deplazes, E & Callaghan, R 2023, 'Biochemical interactions between the Atm1-like transporter from Novosphingobium aromaticivorans and heavy metals', Archives of Biochemistry and Biophysics, vol. 744, pp. 109696-109696.
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Rouet, R, Henry, JY, Johansen, MD, Sobti, M, Balachandran, H, Langley, DB, Walker, GJ, Lenthall, H, Jackson, J, Ubiparipovic, S, Mazigi, O, Schofield, P, Burnett, DL, Brown, SHJ, Martinello, M, Hudson, B, Gilroy, N, Post, JJ, Kelleher, A, Jäck, H-M, Goodnow, CC, Turville, SG, Rawlinson, WD, Bull, RA, Stewart, AG, Hansbro, PM & Christ, D 2023, 'Broadly neutralizing SARS-CoV-2 antibodies through epitope-based selection from convalescent patients', Nature Communications, vol. 14, no. 1, p. 687.
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AbstractEmerging variants of concern (VOCs) are threatening to limit the effectiveness of SARS-CoV-2 monoclonal antibodies and vaccines currently used in clinical practice; broadly neutralizing antibodies and strategies for their identification are therefore urgently required. Here we demonstrate that broadly neutralizing antibodies can be isolated from peripheral blood mononuclear cells of convalescent patients using SARS-CoV-2 receptor binding domains carrying epitope-specific mutations. This is exemplified by two human antibodies, GAR05, binding to epitope class 1, and GAR12, binding to a new epitope class 6 (located between class 3 and 5). Both antibodies broadly neutralize VOCs, exceeding the potency of the clinical monoclonal sotrovimab (S309) by orders of magnitude. They also provide prophylactic and therapeutic in vivo protection of female hACE2 mice against viral challenge. Our results indicate that exposure to SARS-CoV-2 induces antibodies that maintain broad neutralization against emerging VOCs using two unique strategies: either by targeting the divergent class 1 epitope in a manner resistant to VOCs (ACE2 mimicry, as illustrated by GAR05 and mAbs P2C-1F11/S2K14); or alternatively, by targeting rare and highly conserved epitopes, such as the new class 6 epitope identified here (as illustrated by GAR12). Our results provide guidance for next generation monoclonal antibody development and vaccine design.

Rourke, ML, Walburn, JW, Broadhurst, MK, Fowler, AM, Hughes, JM, Fielder, DS, DiBattista, JD & Furlan, EM 2023, 'Poor utility of environmental DNA for estimating the biomass of a threatened freshwater teleost; but clear direction for future candidate assessments', Fisheries Research, vol. 258, pp. 106545-106545.
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Roy Chowdhury, P, Hastak, P, DeMaere, M, Wyrsch, E, Li, D, Elankumaran, P, Dolejska, M, Browning, GF, Marenda, MS, Gottlieb, T, Cheong, E, Merlino, J, Myers, GSA & Djordjevic, SP 2023, 'Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission?', mSystems, vol. 8, no. 5, p. e0123622.
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ABSTRACT We performed a comprehensive phylogenomic analysis of 925 extraintestinal pathogenic Escherichia coli (ExPEC) ST38 genomes from 38 countries and diverse hosts and sources. The phylogeny resolved two broad clades: A (593 strains; 91% human) and B (332 isolates; 42% human), each with distinct ST38 clusters linked to the carriage of specific bla CTX-M alleles, often in association with other antibiotic resistance genes, class 1 integrons and specific plasmid replicon types. Co-carriage of fyuA and irp2 virulence genes, a reliable proxy for carriage of the Yersinia high-pathogenicity island, featured in 580 (62.7%) genomes. ST38 lineages carrying combinations of ExPEC and intestinal pathogenic Escherichia coli virulence factors were also identified. The F plasmid replicon was identified in 536 (58%) genomes, and 112 of these (21%) carry cjrABC-senB , a virulence operon frequently identified in pandemic ExPEC sequence types. Most (108; 96.4%) cjrABC-senB + ST38 isolates were from human and other sources, except food animals, and were associated with F5:A-:B10 (41 isolates), F1:A2:B20 (20 isolates), and F24:A-:B1 (15 isolates) F replicon types. ST38 genomes that were inferred to carry a ColV-F virulence plasmid (69; 7.4%) were mostly from human (12; 17.4%), avian (26; 37.7%), or poultry (10; 6.9%) sources. We identified multiple examples of putative inter-host and host-environment transmission events, where genomes differed by <35 SNPs. This work emphasizes the importance of adopting a One Health approach for ...

Russell, K, Kelty, SF & Scudder, N 2023, 'Public and family support and concerns for providing DNA to law enforcement in long-term missing person cases', Science & Justice, vol. 63, no. 2, pp. 149-157.
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Russell, K, Kelty, SF & Scudder, N 2023, 'Public/family concerns for providing DNA in missing persons cases: Paper 2: The main concerns raised and implications for policing policy', Science & Justice, vol. 63, no. 6, pp. 671-679.
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Ruvindy, R, Barua, A, Bolch, CJS, Sarowar, C, Savela, H & Murray, SA 2023, 'Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms', ISME Communications, vol. 3, no. 1.
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Abstract The application of meta-barcoding, qPCR, and metagenomics to aquatic eukaryotic microbial communities requires knowledge of genomic copy number variability (CNV). CNV may be particularly relevant to functional genes, impacting dosage and expression, yet little is known of the scale and role of CNV in microbial eukaryotes. Here, we quantify CNV of rRNA and a gene involved in Paralytic Shellfish Toxin (PST) synthesis (sxtA4), in 51 strains of 4 Alexandrium (Dinophyceae) species. Genomes varied up to threefold within species and ~7-fold amongst species, with the largest (A. pacificum, 130 ± 1.3 pg cell−1 /~127 Gbp) in the largest size category of any eukaryote. Genomic copy numbers (GCN) of rRNA varied by 6 orders of magnitude amongst Alexandrium (102– 108 copies cell−1) and were significantly related to genome size. Within the population CNV of rRNA was 2 orders of magnitude (105 – 107 cell−1) in 15 isolates from one population, demonstrating that quantitative data based on rRNA genes needs considerable caution in interpretation, even if validated against locally isolated strains. Despite up to 30 years in laboratory culture, rRNA CNV and genome size variability were not correlated with time in culture. Cell volume was only weakly associated with rRNA GCN (20–22% variance explained across dinoflagellates, 4% in Gonyaulacales). GCN of sxtA4 varied from 0–102 copies cell−1, was significantly related to PSTs (ng cell−1), displaying a gene dosage effect modulating PST production. Our data indicate that in dinoflagellates, a major marine eukaryotic group, low-copy functional genes are more reliable and informative targets for quantification of ecological processes than unstable rRNA genes.

Ryan, T, Hooftman, A, Rehill, A, Johansen, M, O’Brien, E, Toller-Kawahisa, J, Day, E, Weiss, H, Peace, C, Zotta, A, Hansbro, N, O’Donnell, J, Hansbro, P, McLoughlin, R, Wygrecka, M, Preston, R, Zasłona, Z & O’Neill, L 2023, 'OC 55.2 Dimethyl Fumarate and 4-Octyl Itaconate are Anticoagulants that Suppress Tissue Factor in Macrophages Via Inhibition of Type I Interferon', Research and Practice in Thrombosis and Haemostasis, vol. 7, pp. 100502-100502.
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Ryan, TAJ, Hooftman, A, Rehill, AM, Johansen, MD, Brien, ECO, Toller-Kawahisa, JE, Wilk, MM, Day, EA, Weiss, HJ, Sarvari, P, Vozza, EG, Schramm, F, Peace, CG, Zotta, A, Miemczyk, S, Nalkurthi, C, Hansbro, NG, McManus, G, O’Doherty, L, Gargan, S, Long, A, Dunne, J, Cheallaigh, CN, Conlon, N, Carty, M, Fallon, PG, Mills, KHG, Creagh, EM, Donnell, JSO, Hertzog, PJ, Hansbro, PM, McLoughlin, RM, Wygrecka, M, Preston, RJS, Zasłona, Z & O’Neill, LAJ 2023, 'Dimethyl fumarate and 4-octyl itaconate are anticoagulants that suppress Tissue Factor in macrophages via inhibition of Type I Interferon', Nature Communications, vol. 14, no. 1, p. 3513.
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AbstractExcessive inflammation-associated coagulation is a feature of infectious diseases, occurring in such conditions as bacterial sepsis and COVID-19. It can lead to disseminated intravascular coagulation, one of the leading causes of mortality worldwide. Recently, type I interferon (IFN) signaling has been shown to be required for tissue factor (TF; gene name F3) release from macrophages, a critical initiator of coagulation, providing an important mechanistic link between innate immunity and coagulation. The mechanism of release involves type I IFN-induced caspase-11 which promotes macrophage pyroptosis. Here we find that F3 is a type I IFN-stimulated gene. Furthermore, F3 induction by lipopolysaccharide (LPS) is inhibited by the anti-inflammatory agents dimethyl fumarate (DMF) and 4-octyl itaconate (4-OI). Mechanistically, inhibition of F3 by DMF and 4-OI involves suppression of Ifnb1 expression. Additionally, they block type I IFN- and caspase-11-mediated macrophage pyroptosis, and subsequent TF release. Thereby, DMF and 4-OI inhibit TF-dependent thrombin generation. In vivo, DMF and 4-OI suppress TF-dependent thrombin generation, pulmonary thromboinflammation, and lethality induced by LPS, E. coli, and S. aureus, with 4-OI additionally attenuating inflammation-associated coagulation in a model of SARS-CoV-2 infection. Our results identify the clinically approved drug DMF and the pre-clinical tool compound 4-OI as anticoagulants that inhibit TF-mediated coagulopathy via inhibition of the macrophage type I IFN-TF axis.

Saerens, G, Dursap, T, Hesner, I, Duong, NMH, Solntsev, AS, Morandi, A, Maeder, A, Karvounis, A, Regreny, P, Chapman, RJ, Danescu, A, Chauvin, N, Penuelas, J & Grange, R 2023, 'Background-Free Near-Infrared Biphoton Emission from Single GaAs Nanowires', Nano Letters, vol. 23, no. 8, pp. 3245-3250.
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Safaei, J, Gao, Y, Hosseinpour, M, Zhang, X, Sun, Y, Tang, X, Zhang, Z, Wang, S, Guo, X, Wang, Y, Chen, Z, Zhou, D, Kang, F, Jiang, L & Wang, G 2023, 'Vacancy Engineering for High-Efficiency Nanofluidic Osmotic Energy Generation', Journal of the American Chemical Society, vol. 145, no. 4, pp. 2669-2678.
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Salih, AK, Phillips, MR & Ton-That, C 2023, 'Enhanced solar-driven water splitting performance using oxygen vacancy rich ZnO photoanodes', Solar Energy Materials and Solar Cells, vol. 259, pp. 112436-112436.
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Salvato, I, Ricciardi, L, Dal Col, J, Nigro, A, Giurato, G, Memoli, D, Sellitto, A, Lamparelli, EP, Crescenzi, MA, Vitale, M, Vatrella, A, Nucera, F, Brun, P, Caicci, F, Dama, P, Stiff, T, Castellano, L, Idrees, S, Johansen, MD, Faiz, A, Wark, PA, Hansbro, PM, Adcock, IM, Caramori, G & Stellato, C 2023, 'Expression of targets of the RNA-binding protein AUF-1 in human airway epithelium indicates its role in cellular senescence and inflammation', Frontiers in Immunology, vol. 14, p. 1192028.
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IntroductionThe RNA-binding protein AU-rich-element factor-1 (AUF-1) participates to posttranscriptional regulation of genes involved in inflammation and cellular senescence, two pathogenic mechanisms of chronic obstructive pulmonary disease (COPD). Decreased AUF-1 expression was described in bronchiolar epithelium of COPD patients versus controls and in vitro cytokine- and cigarette smoke-challenged human airway epithelial cells, prompting the identification of epithelial AUF-1-targeted transcripts and function, and investigation on the mechanism of its loss.ResultsRNA immunoprecipitation-sequencing (RIP-Seq) identified, in the human airway epithelial cell line BEAS-2B, 494 AUF-1-bound mRNAs enriched in their 3’-untranslated regions for a Guanine-Cytosine (GC)-rich binding motif. AUF-1 association with selected transcripts and with a synthetic GC-rich motif were validated by biotin pulldown. AUF-1-targets’ steady-state levels were equally affected by partial or near-total AUF-1 loss induced by cytomix (TNFα/IL1β/IFNγ/10 nM each) and siRNA, respectively, with differential transcript decay rates. Cytomix-mediated decrease in AUF-1 levels in BEAS-2B and primary human small-airways epithelium (HSAEC) was replicated by treatment with the senescence- inducer compound etoposide and associated with readouts of cell-cycle arrest, increase in lysosomal damage and senescence-associated secretory phenotype (SASP) factors, and with AUF-1 transfer in extracellular vesicles, detected by transmission electron microscopy and immunoblotting. Extensive in-silico and genome ontology analysis found, consistent with AUF-1 functions, enriched RIP-Seq-derived AUF-1-targets in COPD-related pathways involved in inflammation, senescence, gene regulation and also in the public SASP proteome atlas; AUF-1 target signature wa...

Sasko, LM, Oliver, B & Smith, SM 2023, 'Fit testing of masks worn by frontline healthcare workers', Infection Control & Hospital Epidemiology, vol. 44, no. 4, pp. 682-684.
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Saunders, M, Gupta, A, Roux, C & Spindler, X 2023, 'The impact of substrate dampness on the transfer of glass fragments to upper garments when breaking windows', Forensic Science International, vol. 350, pp. 111791-111791.
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Saura-Múzquiz, M, Marlton, FP, Mullens, BG, Liu, J, Vogt, T, Maynard-Casely, HE, Avdeev, M, Blom, DA & Kennedy, BJ 2023, 'Cation and Lone Pair Order–Disorder in the Polymorphic Mixed Metal Bismuth Scheelite Bi₃FeMo₂O₁₂', Chemistry of Materials, vol. 35, no. 1, pp. 123-135.
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Scanes, E & Byrne, M 2023, 'Warming and hypoxia threaten a valuable scallop fishery: A warning for commercial bivalve ventures in climate change hotspots', Global Change Biology, vol. 29, no. 8, pp. 2043-2045.
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AbstractMarine molluscs constitute the second largest marine fishery and are often caught in coastal and estuarine habitats. Temperature is increasing in these habitats at a rate greater than predicted, especially in warming “hotspots”. This warming is accompanied by hypoxia in a duo of stressors that threatens coastal mollusc fisheries and aquaculture. Collapses of the northern bay scallop (Argopecten irradians irradians) fisheries on the Atlantic coast of the USA are likely to be driven by rapid rates of coastal warming and may provide an ominous glimpse into the prospects of other coastal mollusc fisheries in climate warming hotspots.

Scanes, E, O’Connor, WA, Seymour, JR, Siboni, N, Parker, LM & Ross, PM 2023, 'Emerging diseases in Australian oysters and the challenges of climate change and uncertain futures', Australian Zoologist.
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ABSTRACT Oysters are a valuable and iconic seafood, deeply rooted in Australian culture. However, oysters have always been vulnerable to disease, with disease outbreaks leading to mass mortality events that regularly cost the oyster aquaculture industry millions of dollars and affect livelihoods. Notably, there is evidence that climate change is rapidly causing the emergence of new diseases alongside the amplification of impacts of existing diseases. This is because warming, acidification and freshening of coastal and estuarine habitats is affecting the three axes of disease; the host, the external environment and the pathogens. Here we explore how climate change is likely to impact all three axes of disease in Australian oyster aquaculture. Climate change is affecting oyster physiology, leading to weaker immune defences that allow for increased susceptibility to viral and bacterial infections. For example, there is evidence that recent heavy rain events precede oyster disease in estuaries. In addition, climate change is increasing the abundance and virulence of bacterial and viral pathogens, potentially resulting in the introduction of novel disease into new habitats. In order to remain viable, we suggest that the Australian oyster industry needs to enhance selective breeding programs currently underway with a diversification of products and research on emerging diseases to ensure resilience in the sector.

Scanes, E, Ross, PM, Seymour, JR, Siboni, N, Dove, MC, O'Connor, WA, Dittes, C & Parker, LM 2023, 'Transgenerational transfer of the microbiome is altered by ocean acidification in oyster larvae', Aquaculture, vol. 565, pp. 739153-739153.
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Ocean acidification will affect marine molluscs, however, transgenerational plasticity (TGP) can ameliorate some effects. Marine molluscs acquire members of their microbiome via the egg, yet we know little about how the microbiome can be influenced by transgenerational exposure to ocean acidification. We exposed adult Sydney Rock oysters (Saccostrea glomerata) from four genotypes to elevated and ambient PCO2 for nine weeks. Larvae were then raised in the same ambient and elevated PCO2 conditions. The relative abundance of bacteria in eggs and larvae were characterised using 16S RNA amplicon sequencing. Parental exposure to elevated PCO2 significantly altered the bacterial community composition of both eggs and larvae, but this was dependent on genotype. Parental exposure to elevated PCO2 caused five core Rhodobacteraceae ASVs to increase in relative abundance, and three Rhodobacteraceae ASVs to decrease in relative abundance. These findings show transfer of maternal microbiomes to larvae is altered by exposure to ocean acidification and this may play a role in TGP.

Scanes, E, Siboni, N, Rees, B & Seymour, JR 2023, 'Acclimation in intertidal animals reduces potential pathogen load and increases survival following a heatwave', iScience, vol. 26, no. 6, pp. 106813-106813.
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Intertidal animals can experience intense heat during a heatwave, leading to mortality. The causes of death for intertidal animals following heatwaves have often been attributed to a breakdown in physiological processes. This, however, contrasts with research in other animals where heatwave mortality is attributed to existing or opportunistic diseases. We acclimated intertidal oysters to four treatment levels, including an antibiotic treatment, and then exposed all treatments to a 50°C heatwave for 2 h, replicating what can be experienced on Australian shorelines. We found that both acclimation and antibiotics increased survival and reduced the presence of potential pathogens. Non-acclimated oysters had a significant shift in their microbiome, with increasing abundances of bacteria from the Vibrio genera, including known potential pathogens. Our results demonstrate that bacterial infection plays a pivotal role in post-heatwave mortality. We anticipate these findings to inform the management of aquaculture and intertidal habitats as climate change intensifies.

Scaramuzzo, G, Nucera, F, Asmundo, A, Messina, R, Mari, M, Montanaro, F, Johansen, MD, Monaco, F, Fadda, G, Tuccari, G, Hansbro, NG, Hansbro, PM, Hansel, TT, Adcock, IM, David, A, Kirkham, P, Caramori, G, Volta, CA & Spadaro, S 2023, 'Cellular and molecular features of COVID-19 associated ARDS: therapeutic relevance', Journal of Inflammation, vol. 20, no. 1, p. 11.
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AbstractThe severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection can be asymptomatic or cause a disease (COVID-19) characterized by different levels of severity. The main cause of severe COVID-19 and death is represented by acute (or acute on chronic) respiratory failure and acute respiratory distress syndrome (ARDS), often requiring hospital admission and ventilator support.The molecular pathogenesis of COVID-19-related ARDS (by now termed c-ARDS) is still poorly understood. In this review we will discuss the genetic susceptibility to COVID-19, the pathogenesis and the local and systemic biomarkers correlated with c-ARDS and the therapeutic options that target the cell signalling pathways of c-ARDS.

Schlögl, E, Skov, JB & Skovmand, D 2023, 'Term Structure Modeling of SOFR: Evaluating the Importance of Scheduled Jumps'.

Schoepf, V, Baumann, JH, Barshis, DJ, Browne, NK, Camp, EF, Comeau, S, Cornwall, CE, Guzmán, HM, Riegl, B, Rodolfo-Metalpa, R & Sommer, B 2023, 'Corals at the edge of environmental limits: A new conceptual framework to re-define marginal and extreme coral communities', Science of The Total Environment, vol. 884, pp. 163688-163688.
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Seong, M, Kondaveeti, S, Choi, G, Kim, S, Kim, J, Kang, M & Jeong, HE 2023, '3D Printable Self-Adhesive and Self-Healing Ionotronic Hydrogels for Wearable Healthcare Devices', ACS Applied Materials & Interfaces, vol. 15, no. 8, pp. 11042-11052.
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Shahnaij, M, Amin, MB, Hoque, MM, Mondol, AS, Rana, KJ, Azmi, IJ & Talukder, KA 2023, 'Characterization of Shigella flexneri Serotype 6 Strains Isolated from Bangladesh and Identification of a New Phylogenetic Cluster', Journal of Bacteriology, vol. 205, no. 4.
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Shigella flexneri serotype 6 is one of the predominant serotypes among shigellosis cases in Bangladesh. Characterization of a novel subserotype of S. flexneri 6 (VI:E1037), agglutinated with type 6-specific antibody and anti-E1037, indicates a unique evolutionary ancestry.

Shao, D, Su, F, Zou, X, Lu, J, Wu, S, Tian, R, Ran, D, Guo, Z & Jin, D 2023, 'Pixel-Level Classification of Five Histologic Patterns of Lung Adenocarcinoma', Analytical Chemistry, vol. 95, no. 5, pp. 2664-2670.
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Sharapova, PR, Kruk, SS & Solntsev, AS 2023, 'Nonlinear Dielectric Nanoresonators and Metasurfaces: Toward Efficient Generation of Entangled Photons', Laser & Photonics Reviews, vol. 17, no. 4, pp. 2200408-2200408.
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AbstractAmong the most prominent effects resulting from nonlinear light–matter interaction is the generation of correlated and entangled photons through various processes, notably via spontaneous parametric down‐conversion or spontaneous four‐wave mixing. Such nonlinear optical processes benefit from the concentration of electromagnetic fields in small volumes. Dielectric nanoresonators and their 2D layouts—metasurfaces—provide efficient ways to control light in subwavelength volumes enabling the enhancement of nonlinear light–matter interaction and the generation of entangled photons. Nanoresonators and metasurfaces offer a radical miniaturization of quantum light sources allowing better scalability, which opens a pathway toward arrangements of photon sources in complex subwavelength configurations for advanced photon state control. In this work, the recent progress in this emergent area of research is reviewed.

Shiraki, S, Kamiya, Y, Mehraj, H, Takahashi, S, Seki, M, Dennis, ES & Fujimoto, R 2023, 'The role of histone modification in gene expression in Brassica rapa vegetables', Acta Horticulturae, no. 1362, pp. 107-112.
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Shrestha, J, Paudel, KR, Nazari, H, Dharwal, V, Bazaz, SR, Johansen, MD, Dua, K, Hansbro, PM & Warkiani, ME 2023, 'Advanced models for respiratory disease and drug studies', Medicinal Research Reviews, vol. 43, no. 5, pp. 1470-1503.
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AbstractThe global burden of respiratory diseases is enormous, with many millions of people suffering and dying prematurely every year. The global COVID‐19 pandemic witnessed recently, along with increased air pollution and wildfire events, increases the urgency of identifying the most effective therapeutic measures to combat these diseases even further. Despite increasing expenditure and extensive collaborative efforts to identify and develop the most effective and safe treatments, the failure rates of drugs evaluated in human clinical trials are high. To reverse these trends and minimize the cost of drug development, ineffective drug candidates must be eliminated as early as possible by employing new, efficient, and accurate preclinical screening approaches. Animal models have been the mainstay of pulmonary research as they recapitulate the complex physiological processes, Multiorgan interplay, disease phenotypes of disease, and the pharmacokinetic behavior of drugs. Recently, the use of advanced culture technologies such as organoids and lung‐on‐a‐chip models has gained increasing attention because of their potential to reproduce human diseased states and physiology, with clinically relevant responses to drugs and toxins. This review provides an overview of different animal models for studying respiratory diseases and evaluating drugs. We also highlight recent progress in cell culture technologies to advance integrated models and discuss current challenges and present future perspectives.

Sikkema, L, Ramírez-Suástegui, C, Strobl, DC, Gillett, TE, Zappia, L, Madissoon, E, Markov, NS, Zaragosi, L-E, Ji, Y, Ansari, M, Arguel, M-J, Apperloo, L, Banchero, M, Bécavin, C, Berg, M, Chichelnitskiy, E, Chung, M-I, Collin, A, Gay, ACA, Gote-Schniering, J, Hooshiar Kashani, B, Inecik, K, Jain, M, Kapellos, TS, Kole, TM, Leroy, S, Mayr, CH, Oliver, AJ, von Papen, M, Peter, L, Taylor, CJ, Walzthoeni, T, Xu, C, Bui, LT, De Donno, C, Dony, L, Faiz, A, Guo, M, Gutierrez, AJ, Heumos, L, Huang, N, Ibarra, IL, Jackson, ND, Kadur Lakshminarasimha Murthy, P, Lotfollahi, M, Tabib, T, Talavera-López, C, Travaglini, KJ, Wilbrey-Clark, A, Worlock, KB, Yoshida, M, Chen, Y, Hagood, JS, Agami, A, Horvath, P, Lundeberg, J, Marquette, C-H, Pryhuber, G, Samakovlis, C, Sun, X, Ware, LB, Zhang, K, van den Berge, M, Bossé, Y, Desai, TJ, Eickelberg, O, Kaminski, N, Krasnow, MA, Lafyatis, R, Nikolic, MZ, Powell, JE, Rajagopal, J, Rojas, M, Rozenblatt-Rosen, O, Seibold, MA, Sheppard, D, Shepherd, DP, Sin, DD, Timens, W, Tsankov, AM, Whitsett, J, Xu, Y, Banovich, NE, Barbry, P, Duong, TE, Falk, CS, Meyer, KB, Kropski, JA, Pe’er, D, Schiller, HB, Tata, PR, Schultze, JL, Teichmann, SA, Misharin, AV, Nawijn, MC, Luecken, MD & Theis, FJ 2023, 'An integrated cell atlas of the lung in health and disease', Nature Medicine, vol. 29, no. 6, pp. 1563-1577.
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AbstractSingle-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.

Siwakoti, P, Rennie, C, Huang, Y, Li, JJ, Tuch, BE, McClements, L & Xu, X 2023, 'Challenges with Cell-based Therapies for Type 1 Diabetes Mellitus', Stem Cell Reviews and Reports, vol. 19, no. 3, pp. 601-624.
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Type 1 diabetes (T1D) is a chronic, lifelong metabolic disease. It is characterised by the autoimmune-mediated loss of insulin-producing pancreatic β cells in the islets of Langerhans (β-islets), resulting in disrupted glucose homeostasis. Administration of exogenous insulin is the most common management method for T1D, but this requires lifelong reliance on insulin injections and invasive blood glucose monitoring. Replacement therapies with beta cells are being developed as an advanced curative treatment for T1D. Unfortunately, this approach is limited by the lack of donated pancreatic tissue, the difficulties in beta cell isolation and viability maintenance, the longevity of the transplanted cells in vivo, and consequently high costs. Emerging approaches to address these limitations are under intensive investigations, including the production of insulin-producing beta cells from various stem cells, and the development of bioengineered devices including nanotechnologies for improving islet transplantation efficacy without the need for recipients taking toxic anti-rejection drugs. These emerging approaches present promising prospects, while the challenges with the new techniques need to be tackled for ultimately clinical treatment of T1D. This review discussed the benefits and limitations of the cell-based therapies for beta cell replacement as potential curative treatment for T1D, and the applications of bioengineered devices including nanotechnology to overcome the challenges associated with beta cell transplantation.

Smith, HS, Irga, PJ, Fleck, R & Torpy, FR 2023, 'Portable botanical biofilters to address internal combustion engine exhaust exposure', Building and Environment, vol. 244, pp. 110777-110777.
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Song, A, Song, S, Duanmu, M, Tian, H, Liu, H, Qin, X, Shao, G & Wang, G 2023, 'Recent Progress of Non‐Noble Metallic Heterostructures for the Electrocatalytic Hydrogen Evolution', Small Science, vol. 3, no. 9.
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Developing energy production, storage, and conversion technologies based on sustainable or renewable energy is essential to address the energy and environmental crisis. Electrochemical water splitting is one of the most promising approaches to realize the production of green hydrogen. The design of catalytic materials with low cost, high activity, and long‐term stability and the exploration of specific reaction mechanisms are the key focus for the involved electrochemical hydrogen evolution reaction (HER). Recently, substantial efforts have been devoted to the rational design and synthesis of non‐noble metallic heterostructures with fascinating synergistic effects among different components. These heterostructured materials demonstrate comprehensive properties exceeding the estimations by the rule of mixtures and display high activity and long‐term stability in industrial conditions for HER. Herein, the reaction mechanism and key parameters for improving catalytic performance in the HER process are discussed in detail. The latest advances in heterostructures based on synthetic methods and electrocatalytic characteristics from experimental and computational perspectives are summarized according to the role of various components. Herein, insights are provided in this review into an in‐depth understanding of the heterostructures as HER electrocatalysts, and the opportunities and challenges to scale up future‐oriented developments are highlighted.

Song, P, Li, J, Zhang, Y, Tang, F, Wang, C, Su, D & Wang, T 2023, 'Design of double-shelled NiS-FeS@NC hollow nanocubes for high-performance sodium-ion batteries', Journal of Alloys and Compounds, vol. 950, pp. 169905-169905.
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Speer, MS & Leslie, LM 2023, 'Application of Machine Learning Techniques to Detect and Understand the Impacts of Global Warming on Southeast Australia', Georgetown Journal of International Affairs, vol. 24, no. 2, pp. 260-266.
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Abstract: Australia is adversely affected by global warming (GW), as its well-known cycles of droughts, floods, and extreme weather events are increasingly amplified by GW. Here, the focus is the impacts of GW on populous southeast Australia. Machine Learning attribution techniques have been applied to identify the main drivers of these impacts. This article presents the detection examples of the most relevant drivers, individually and in combination, responsible for observed trends in precipitation and temperature due to GW.

Spencer, L, Horder, J, Kim, S, Toth, M & Aharonovich, I 2023, 'Monolithic Integration of Single Quantum Emitters in hBN Bullseye Cavities', ACS Photonics, vol. 10, no. 12, pp. 4417-4424.
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Steiner, R, Moret, S & Roux, C 2023, 'Production of artificial fingermarks. Part II – The use of a modified inkjet printer for the deposition of synthetic secretions', Forensic Science International, vol. 350, pp. 111804-111804.
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Stelling-Wood, TP, Gribben, PE, Birch, G, Bishop, MJ, Blount, C, Booth, DJ, Brown, C, Bruce, E, Bugnot, AB, Byrne, M, Creese, RG, Dafforn, KA, Dahlenburg, J, Doblin, MA, Fellowes, TE, Fowler, AM, Gibbs, MC, Glamore, W, Glasby, TM, Hay, AC, Kelaher, B, Knott, NA, Larkum, AWD, Parker, LM, Marzinelli, EM, Mayer-Pinto, M, Morgan, B, Murray, SA, Rees, MJ, Ross, PM, Roughan, M, Saintilan, N, Scanes, E, Seymour, JR, Schaefer, N, Suthers, IM, Taylor, MD, Williamson, JE, Vila Concejo, A, Whittington, RJ & Figueira, WF 2023, 'A deep dive into the ecology of Gamay (Botany Bay, Australia): current knowledge and future priorities for this highly modified coastal waterway', Marine and Freshwater Research, vol. 74, no. 12, pp. 1003-1025.
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Context Gamay is a coastal waterway of immense social, cultural and ecological value. Since European settlement, it has become a hub for industrialisation and human modification. There is growing desire for ecosystem-level management of urban waterways, but such efforts are often challenged by a lack of integrated knowledge. Aim and methods We systematically reviewed published literature and traditional ecological knowledge (TEK), and consulted scientists to produce a review of Gamay that synthesises published knowledge of Gamay’s aquatic ecosystem to identify knowledge gaps and future research opportunities. Key results We found 577 published resources on Gamay, of which over 70% focused on ecology. Intertidal rocky shores were the most studied habitat, focusing on invertebrate communities. Few studies considered multiple habitats or taxa. Studies investigating cumulative human impacts, long-term trends and habitat connectivity are lacking, and the broader ecological role of artificial substrate as habitat in Gamay is poorly understood. TEK of Gamay remains a significant knowledge gap. Habitat restoration has shown promising results and could provide opportunities to improve affected habitats in the future. Conclusion and implications This review highlights the extensive amount of knowledge that exists for Gamay, but also identifies key gaps that need to be filled for effective management.

Strudwick, P, Seymour, J, Camp, EF, Roper, C, Edmondson, J, Howlett, L & Suggett, DJ 2023, 'Bacterial communities associated with corals out-planted on the Great Barrier Reef are inherently dynamic over space and time', Marine Biology, vol. 170, no. 7.
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AbstractCoral propagation and out-planting are becoming commonly adopted as part of reef stewardship strategies aimed at improving reef resilience through enhanced natural recovery and rehabilitation. The coral microbiome has a crucial role in the success of the coral holobiont and can be impacted shortly after out-planting. However, long-term characterisation of the out-plant microbiome in relation to out-plant survival, and how these properties vary across reef sites, is unexplored. Therefore, at three reef sites on Opal Reef, Great Barrier Reef (Mojo, Sandbox and Rayban, 16°12′18″S 145°53′54″E), we examined bacterial communities associated with out-planted Acropora millepora coral and monitored coral survival over 12 months (February 2021–22). Bacterial communities of out-planted corals exhibited significant changes from donor colonies 7 days to 1.5 months after out-planting. Further, bacterial community composition differed for sites Sandbox and Rayban with low overall survival (0–43%) versus Mojo with higher overall survival (47–75%). After initial dissimilarity in bacterial communities of out-plants across sites at 1.5 months, and despite changes within sites over time, out-plants exhibited similar microbial communities across sites at 7 days and 6, 9 and 12 months. We hypothesise these trends reflect how bacterial communities are shaped by rapid changes in local environmental characteristics (e.g. from source to out-planting site), where out-plant bacterial communities ‘conform’ to out-planting site conditions. After initial changes, out-plant bacterial communities may then be under the influence of global environmental conditions—such as annual trends in temperature across seasons. Such outcomes indicate the importance of site selection in shaping initial coral bacterial communities and subsequent out-plant success. Importantly, continued differences in out-plant survival trajectory but...

Strutt, JPB, Natarajan, M, Lee, E, Teo, DBL, Sin, W-X, Cheung, K-W, Chew, M, Thazin, K, Barone, PW, Wolfrum, JM, Williams, RBH, Rice, SA & Springs, SL 2023, 'Machine learning-based detection of adventitious microbes in T-cell therapy cultures using long-read sequencing', Microbiology Spectrum, vol. 11, no. 5, p. e0135023.
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ABSTRACT Assuring that cell therapy products are safe before releasing them for use in patients is critical. Currently, compendial sterility testing for bacteria and fungi can take 7–14 days. The goal of this work was to develop a rapid untargeted approach for the sensitive detection of microbial contaminants at low abundance from low volume samples during the manufacturing process of cell therapies. We developed a long-read sequencing methodology using Oxford Nanopore Technologies MinION platform with 16S and 18S amplicon sequencing to detect USP <71> organisms and other microbial species. Reads are classified metagenomically to predict the microbial species. We used an extreme gradient boosting machine learning algorithm (XGBoost) to first assess if a sample is contaminated, and second, determine whether the predicted contaminant is correctly classified or misclassified. The model was used to make a final decision on the sterility status of the input sample. An optimized experimental and bioinformatics pipeline starting from spiked species through to sequenced reads allowed for the detection of microbial samples at 10 colony-forming units (CFU)/mL using metagenomic classification. Machine learning can be coupled with long-read sequencing to detect and identify sample sterility status and microbial species present in T-cell cultures, including the USP <71> organisms to 10 CFU/mL. IMPORTANCE This research presents a novel method for rapidly and accurately detecting microbial contaminants in cell therapy products, which is essential for ensuring patient safety. Traditional testing methods are time-consuming, taking 7–14 days, while our approach can significantly reduce this time. By combining advanced long-read nanopore sequencing techniques and machine learning, we can effectively identify the presence and types o...

Studholme, SJ, Heywood, ZE, Mallinson, JB, Steel, JK, Bones, PJ, Arnold, MD & Brown, SA 2023, 'Computation via Neuron-like Spiking in Percolating Networks of Nanoparticles', Nano Letters, vol. 23, no. 22, pp. 10594-10599.
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Su, Y, Hu, X, Kang, Y, Zhang, C, Cheng, YY, Jiao, Z, Nie, Y & Song, K 2023, 'Curcumin nanoparticles combined with 3D printed bionic tumor models for breast cancer treatment', Biofabrication, vol. 15, no. 1, pp. 014105-014105.
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Abstract Compared with conventional therapeutic approaches, nanomedicines are attracting a growing interest due to their better targeting ability, higher delivery efficiency, and good water solubility. However, conventional drug efficacy assessment methods are based on a two-dimensional (2D) culture approach of single cells to obtain in vitro therapeutic effects, which may not be representative of actual tumors. Based on the above considerations, the three-dimensional (3D) cell culture models became a better choice since they can increase the complexity of in vitro systems and provide a biomimetic microenvironment that is closer to the in vivo native than 2D cultures. In our study, curcumin nanoparticle (CurNPs) with good water solubility and good tumor therapeutic effects were prepared by combining polymeric non-ionic surfactant (Pluronic F127) with curcumin. The hybrid scaffolds based on nano-clay, sodium alginate, and gelatin were also prepared, which showed good printability and excellent biocompatibility. We then studied the therapeutic effects of CurNPs on metastatic breast cancer using a 3D tumor model fabricated with scaffold-bound metastatic breast cancer (MDA-MB-231) cells. It was showed that the 3D cell model presented better cell proliferation effect while compared with 2D version. Additionally, there was good enhanced permeability and retention effect when CurNPs entered with better accumulate in 3D cell ‘tumor’ sites which represented more realistic response of a more real tumor treatment effect for breast cancer cells. Our study indicated that the combinational of nanomaterials with 3D cell ‘tumor’ models provided an alternative and better platform for drug screening and has great potential be used as safe and effective treatment screening for breast cancer.

Suggett, DJ, Edwards, M, Cotton, D, Hein, M & Camp, EF 2023, 'An integrative framework for sustainable coral reef restoration', One Earth, vol. 6, no. 6, pp. 666-681.
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Sulaiman, I, Wu, BG, Chung, M, Isaacs, B, Tsay, J-CJ, Holub, M, Barnett, CR, Kwok, B, Kugler, MC, Natalini, JG, Singh, S, Li, Y, Schluger, R, Carpenito, J, Collazo, D, Perez, L, Kyeremateng, Y, Chang, M, Campbell, CD, Hansbro, PM, Oppenheimer, BW, Berger, KI, Goldring, RM, Koralov, SB, Weiden, MD, Xiao, R, D’Armiento, J, Clemente, JC, Ghedin, E & Segal, LN 2023, 'Lower Airway Dysbiosis Augments Lung Inflammatory Injury in Mild-to-Moderate Chronic Obstructive Pulmonary Disease', American Journal of Respiratory and Critical Care Medicine, vol. 208, no. 10, pp. 1101-1114.
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Sun, Y, Kong, M, Ke, J, Yuan, W, Wen, C, Gu, Y, Luo, S & Feng, W 2023, 'Nanothermometer for In Vivo Temperature Detection with High Spatial Resolution Based on Core–Shell Rare Earth Nanoparticles', ACS Applied Nano Materials, vol. 6, no. 24, pp. 23173-23183.
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Suzzi, AL, Stat, M, Gaston, TF, Siboni, N, Williams, NLR, Seymour, JR & Huggett, MJ 2023, 'Elevated estuary water temperature drives fish gut dysbiosis and increased loads of pathogenic vibrionaceae', Environmental Research, vol. 219, pp. 115144-115144.
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Szpila, K, Piwczyński, M, Glinkowski, W, Lutz, L, Akbarzadeh, K, Baz, A, Johnston, NP & Grzywacz, A 2023, 'First molecular phylogeny and species delimitation of West PalaearcticPollenia(Diptera: Polleniidae)', Zoological Journal of the Linnean Society, vol. 197, no. 1, pp. 267-282.
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AbstractCluster flies of the genus Pollenia are known as mass invaders of human dwellings, but are important plant pollinators in the temperate climatic zone. Despite being the most species-rich and widespread genus in Polleniidae, no study to date has tested infrageneric relationships using molecular data. Here we use three molecular markers, COI, Ef-1α and CAD to reconstruct the phylogenetic relationships between 18 West Palaearctic species of Pollenia, representing eight predefined morphological species groups, using both maximum likelihood and Bayesian approaches. We show several instances where morphological and molecular results are congruent, but also instances where they are discordant. We develop a COI barcode reference library for 18 species, containing newly generated data (87 sequences) and sequences retrieved from the Barcode of Life Data System (BOLD). We analyse this dataset using both Automatic Barcode Gap Discovery (ABGD) and Bayesian Phylogenetics & Phylogeography (BPP) methods to validate morphological species hypotheses and delimit species. The results of these species delimitation analyses were, in most cases, identical and aligned with predefined morphological species concepts. Based on the results of our analyses, we synonymize P. moravica (stat. rev.) with P. amentaria and assign 191 unidentified sequences from BOLD to named morphospecies.

Tan, TH, Zhang, H, Xie, B, Mann, R, Peng, L, Yun, SLJ, Amal, R, Gu, Z & Gunawan, C 2023, 'Hydroxyl Radical Generating Monovalent Copper Particles for Antimicrobial Application', Journal of Nanomaterials, vol. 2023, pp. 1-10.
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The antimicrobial properties of copper are well-known but maintaining a low oxidation state of Cu in particles is difficult. Herein, antimicrobial CuxP particles were synthesized through phosphorization of Cu(OH)2, to lock copper in its monovalent state (as Cu3P). We found that the phosphorization could be achieved at temperatures as low as 200°C, with stable surface presence of Cu(I) on the resulting CuxP particles. Cu(I) can act as a one-electron reducing agent for molecular oxygen, to generate the highly reactive hydroxyl radical. In this study, CuxP displayed antibacterial activities on the Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli, with minimum inhibitory concentrations of 32 mg/L for the highest temperature particles (350°C) on both model bacteria. The evident membrane damage is consistent with the intended hydroxyl radical bacterial targeting mechanism. Low-temperature CuxP, although exhibiting lower antibacterial efficacies than those of the higher temperature variant, still showed competitive growth inhibiting activities when compared to other reported antimicrobial copper-based particles. The present work showcases advancements in particle technology that can lead to the development of a more robust antimicrobial agent, presenting a potent additive for self-disinfection applications.

Tang, Q, Xue, N, Ding, X, Tsai, KH-Y, Hew, JJ, Jiang, R, Huang, R, Cheng, X, Ding, X, Yee Cheng, Y, Chen, J & Wang, Y 2023, 'Role of wound microbiome, strategies of microbiota delivery system and clinical management', Advanced Drug Delivery Reviews, vol. 192, pp. 114671-114671.
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Tang, S-J, Zhang, M, Sun, J, Meng, J-W, Xiong, X, Gong, Q, Jin, D, Yang, Q-F & Xiao, Y-F 2023, 'Single-particle photoacoustic vibrational spectroscopy using optical microresonators', Nature Photonics, vol. 17, no. 11, pp. 951-956.
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Tanvet, C, Camp, EF, Sutton, J, Houlbrèque, F, Thouzeau, G & Rodolfo‐Metalpa, R 2023, 'Corals adapted to extreme and fluctuating seawater pH increase calcification rates and have unique symbiont communities', Ecology and Evolution, vol. 13, no. 5.
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AbstractOcean acidification (OA) is a severe threat to coral reefs mainly by reducing their calcification rate. Identifying the resilience factors of corals to decreasing seawater pH is of paramount importance to predict the survivability of coral reefs in the future. This study compared corals adapted to variable pHT (i.e., 7.23–8.06) from the semi‐enclosed lagoon of Bouraké, New Caledonia, to corals adapted to more stable seawater pHT (i.e., 7.90–8.18). In a 100‐day aquarium experiment, we examined the physiological response and genetic diversity of Symbiodiniaceae from three coral species (Acropora tenuis, Montipora digitata, and Porites sp.) from both sites under three stable pHNBS conditions (8.11, 7.76, 7.54) and one fluctuating pHNBS regime (between 7.56 and 8.07). Bouraké corals consistently exhibited higher growth rates than corals from the stable pH environment. Interestingly, A. tenuis from Bouraké showed the highest growth rate under the 7.76 pHNBS condition, whereas for M. digitata, and Porites sp. from Bouraké, growth was highest under the fluctuating regime and the 8.11 pHNBS conditions, respectively. While OA generally decreased coral calcification by ca. 16%, Bouraké corals showed higher growth rates than corals from the stable pH environment (21% increase for A. tenuis to 93% for M. digitata, with all pH conditions pooled). This superior performance coincided with divergent symbiont communities that were more homogenous for Bouraké corals. Corals adapted to variable pH conditions appear to have a better capacity to calcify under reduced pH compared to corals native to...

Tapas, MJ, Thomas, P, Vessalas, K, Nsiah-Baafi, E, Martin, L & Sirivivatnanon, V 2023, 'Comparative study of the efficacy of fly ash and reactive aggregate powders in mitigating alkali-silica reaction', Journal of Building Engineering, vol. 63, pp. 105571-105571.
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Thakur, S, Satija, S, Srivastava, N & Khurana, N 2023, 'HPTLC Method for Boswellic Acids', Current Trends in Biotechnology and Pharmacy, vol. 17, no. 3, pp. 997-1003.
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Boswelliic acids (BAs) are derived from the Boswellia serrata oleo gum resin and used as potential anti-inflammatory, pituitary, immu-nomodulatory, and antitumor experts. The aim of the current study is to evaluate KBA and AKBA separately by high performance thin film chromatography (HPTLC) in Boswellia serrata. For the simultaneous quantification of boswellic acids, an HPTLC method was employed; 11-ke-to-β-boswellic acid (KBA) and 3-acetyl-11-ke-to-β-boswellic acid (AKBA) at 254 nm.

Thaler, M, Wang, Y, van der Does, AM, Faiz, A, Ninaber, DK, Ogando, NS, Beckert, H, Taube, C, Salgado-Benvindo, C, Snijder, EJ, Bredenbeek, PJ, Hiemstra, PS & van Hemert, MJ 2023, 'Impact of Changes in Human Airway Epithelial Cellular Composition and Differentiation on SARS-CoV-2 Infection Biology', Journal of Innate Immunity, vol. 15, no. 1, pp. 562-580.
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The consequences of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can range from asymptomatic to fatal disease. Variations in epithelial susceptibility to SARS-CoV-2 infection depend on the anatomical location from the proximal to distal respiratory tract. However, the cellular biology underlying these variations is not completely understood. Thus, air-liquid interface cultures of well-differentiated primary human tracheal and bronchial epithelial cells were employed to study the impact of epithelial cellular composition and differentiation on SARS-CoV-2 infection by transcriptional (RNA sequencing) and immunofluorescent analyses. Changes of cellular composition were investigated by varying time of differentiation or by using specific compounds. We found that SARS-CoV-2 primarily infected not only ciliated cells but also goblet cells and transient secretory cells. Viral replication was impacted by differences in cellular composition, which depended on culturing time and anatomical origin. A higher percentage of ciliated cells correlated with a higher viral load. However, DAPT treatment, which increased the number of ciliated cells and reduced goblet cells, decreased viral load, indicating the contribution of goblet cells to infection. Cell entry factors, especially cathepsin L and transmembrane protease serine 2, were also affected by differentiation time. In conclusion, our study demonstrates that viral replication is affected by changes in cellular composition, especially in cells related to the mucociliary system. This could explain in part the variable susceptibility to SARS-CoV-2 infection between individuals and between anatomical locations in the respiratory tract.

Thanh, NL, Nguyet, NLH, Le, VG, Thuy, NT, Phong, VHN, Que, VNX, Hang, VT & Huy, NN 2023, 'Optimization process for enhancing the recovery of ammonium and phosphate from wastewater by modified rice husk biochar', Engineering and Applied Science Research, vol. 50, no. 2, pp. 185-194.
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This study aimed to optimize the recovery of ammonium and phosphate from wastewater using Mg-modified biochar as an adsorbent. Given the situation of domestic wastewater and agricultural waste in Vietnam, the researchers fabricated biochar from rice husk and modified it with magnesium salt to make it an effective material for wastewater treatment. To determine the optimal conditions for the experiments, the response surface methodology was used, specifically the central composite design (CCD) model with four factors, namely biochar dosage (g/L), pH, N:P ratio, and initial concentrations of NH4+ and PO43-. The material was thoroughly characterized using scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), energy-dispersive X-ray spectroscopy (EDS), and X-ray diffraction (XRD) to ensure that it met the desired specifications. Based on the experimental design, the optimal conditions were determined to be a biochar dosage of 0.12 g/L, an N:P ratio of 1.25, an initial concentration of 60 mg/L, and a pH of 6. Tests conducted in synthetic wastewater produced results that were in agreement with the predicted values. However, when the optimized values were tested in domestic wastewater, only phosphate removal showed good agreement with an efficiency of 93% compared to the predicted optimization value of 88%. This study demonstrates the potential of Mg-modified biochar as an effective adsorbent for recovering ammonium and phosphate from wastewater. Although further optimization may be required for ammonium removal in domestic wastewater, the results are promising and warrant further investigation.

Tian, C, Li, X-Y, Nelson, VE, Ou, P, Zhou, D, Chen, Y, Zhang, J, Huang, JE, Wang, N, Yu, J, Liu, H, Liu, C, Yang, Y, Peng, T, Zhao, Y, Lee, B-H, Wang, S, Shirzadi, E, Chen, Z, Miao, RK, Sinton, D & Sargent, EH 2023, 'Paired Electrosynthesis of H₂ and Acetic Acid at A/cm² Current Densities', ACS Energy Letters, vol. 8, no. 10, pp. 4096-4103.
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Tian, H, Song, A, Zhang, P, Sun, K, Wang, J, Sun, B, Fan, Q, Shao, G, Chen, C, Liu, H, Li, Y & Wang, G 2023, 'High Durability of Fe–N–C Single‐Atom Catalysts with Carbon Vacancies toward the Oxygen Reduction Reaction in Alkaline Media', Advanced Materials, vol. 35, no. 14, pp. 2210714-2210714.
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AbstractSingle‐atom catalysts (SACs) have attracted extensive interest to catalyze the oxygen reduction reaction (ORR) in fuel cells and metal–air batteries. However, the development of SACs with high selectivity and long‐term stability is a great challenge. In this work, carbon vacancy modified Fe–N–C SACs (FeH–N–C) are practically designed and synthesized through microenvironment modulation, achieving high‐efficient utilization of active sites and optimization of electronic structures. The FeH–N–C catalyst exhibits a half‐wave potential (E1/2) of 0.91 V and sufficient durability of 100 000 voltage cycles with 29 mV E1/2 loss. Density functional theory (DFT) calculations confirm that the vacancies around metal–N4 sites can reduce the adsorption free energy of OH*, and hinder the dissolution of metal center, significantly enhancing the ORR kinetics and stability. Accordingly, FeH–N–C SACs presented a high‐power density and long‐term stability over 1200 h in rechargeable zinc–air batteries (ZABs). This work will not only guide for developing highly active and stable SACs through rational modulation of metal–N4 sites, but also provide an insight into the optimization of the electronic structure to boost electrocatalytical performances.

Tran, T, Ho-Le, T, Bliuc, D, Abrahamsen, B, Hansen, L, Vestergaard, P, Center, JR & Nguyen, TV 2023, '‘Skeletal Age’ for mapping the impact of fracture on mortality', eLife, vol. 12, p. e83888.
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Background:Fragility fracture is associated with an increased risk of mortality, but mortality is not part of doctor-patient communication. Here, we introduce a new concept called ‘Skeletal Age’ as the age of an individual’s skeleton resulting from a fragility fracture to convey the combined risk of fracture and fracture-associated mortality for an individual.Methods:We used the Danish National Hospital Discharge Register which includes the whole-country data of 1,667,339 adults in Denmark born on or before January 1, 1950, who were followed up to December 31, 2016 for incident low-trauma fracture and mortality. Skeletal age is defined as the sum of chronological age and the number of years of life lost (YLL) associated with a fracture. Cox’s proportional hazards model was employed to determine the hazard of mortality associated with a specific fracture for a given risk profile, and the hazard was then transformed into YLL using the Gompertz law of mortality.Results:During the median follow-up period of 16 years, there had been 307,870 fractures and 122,744 post-fracture deaths. A fracture was associated with between 1 and 7 years of life lost, with the loss being greater in men than women. Hip fractures incurred the greatest loss of life years. For instance, a 60-year-old individual with a hip fracture is estimated to have a skeletal age of 66 for men and 65 for women. Skeletal Age was estimated for each age and fracture site stratified by gender.Conclusions:We propose ‘Skeletal Age’ as a new metric to assess the impact of a fragility fracture on an individual’s life expectancy. This approach will enhance doctor-patient risk communication about the risks associated with osteoporosis.

Tran, TN, Gale, A, Whitefield, B, Dyakonov, V, Toth, M, Aharonovich, I & Kianinia, M 2023, 'Coupling spin defects in hexagonal boron nitride to a microwave cavity', Applied Physics Letters, vol. 123, no. 3.
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Optically addressable spin defects in hexagonal boron nitride (hBN) have become a promising platform for quantum sensing. While sensitivity of these defects is limited by their interactions with the spin environment in hBN, inefficient microwave delivery can further reduce their sensitivity. Here, we design and fabricate a microwave double arc resonator for efficient transferring of the microwave field at 3.8 GHz. The spin transitions in the ground state of VB− are coupled to the frequency of the microwave cavity, which result in enhanced optically detected magnetic resonance (ODMR) contrast. In addition, the linewidth of the ODMR signal further reduces, achieving a magnetic field sensitivity as low as 42.4 μT/√Hz. Our robust and scalable device engineering is promising for future employment of spin defects in hBN for quantum sensing.

Tran, TS, Ho-Le, TP, Bliuc, D, Center, JR, Blank, RD & Nguyen, TV 2023, 'Prevention of Hip Fractures: Trade-off between Minor Benefits to Individuals and Large Benefits to the Community', Journal of Bone and Mineral Research, vol. 38, no. 11, pp. 1594-1602.
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ABSTRACT Goeffrey Rose postulated that a population-based measure bringing a small benefit to each individual can yield large benefits to the community. We aimed to test this axiom by quantifying the relationship between change in bone mineral density (BMD) and hip fracture incidence between two prospective cohorts separated by ~10 years. In this prospective population-based Dubbo Osteoporosis Epidemiology Study (DOES), the participants aged 60+ were recruited in two waves: the initial cohort (1311 women, 842 men) in 1989 to 1992 and the second cohort (974 women, 544 men) in 1999 to 2001. The incident hip fracture was radiologically ascertained. Femoral neck BMD was measured biannually. Multivariable-adjusted Cox's proportional hazards models were adjusted for the predefined covariates such as age, BMI, lifestyle factors, falls, and prior fracture. Compared with the initial cohort, the second cohort had a higher femoral neck BMD by ~0.04 g/cm2 in women and 0.03 g/cm2 in men. However, the prevalence of osteoporosis in the second cohort was halved (prevalence ratio 0.51, 95% CI 0.36 to 0.73 in women; 0.45, 0.24 to 0.84 in men), and its hip fracture incidence was significantly reduced (hazard ratio 0.54, 95% CI, 0.38 to 0.78 in women; 0.39, 0.19 to 0.80 in men). Sensitivity analyses indicated that the “effect” was unlikely due to unmeasured confounders. These findings suggest that a population-wide strategy aimed at enhancing BMD across the entire population could lead to a substantial decrease in the incidence of hip fractures. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

Travis, G, McGowan, EM, Simpson, AM, Marsh, DJ & Nassif, NT 2023, 'PTEN, PTENP1, microRNAs, and ceRNA Networks: Precision Targeting in Cancer Therapeutics', Cancers, vol. 15, no. 20, pp. 4954-4954.
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The phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a well characterised tumour suppressor, playing a critical role in the maintenance of fundamental cellular processes including cell proliferation, migration, metabolism, and survival. Subtle decreases in cellular levels of PTEN result in the development and progression of cancer, hence there is tight regulation of the expression, activity, and cellular half-life of PTEN at the transcriptional, post-transcriptional, and post-translational levels. PTENP1, the processed pseudogene of PTEN, is an important transcriptional and post-transcriptional regulator of PTEN. PTENP1 expression produces sense and antisense transcripts modulating PTEN expression, in conjunction with miRNAs. Due to the high sequence similarity between PTEN and the PTENP1 sense transcript, the transcripts possess common miRNA binding sites with the potential for PTENP1 to compete for the binding, or ‘sponging’, of miRNAs that would otherwise target the PTEN transcript. PTENP1 therefore acts as a competitive endogenous RNA (ceRNA), competing with PTEN for the binding of specific miRNAs to alter the abundance of PTEN. Transcription from the antisense strand produces two functionally independent isoforms (PTENP1-AS-α and PTENP1-AS-β), which can regulate PTEN transcription. In this review, we provide an overview of the post-transcriptional regulation of PTEN through interaction with its pseudogene, the cellular miRNA milieu and operation of the ceRNA network. Furthermore, its importance in maintaining cellular integrity and how disruption of this PTEN–miRNA–PTENP1 axis may lead to cancer but also provide novel therapeutic opportunities, is discussed. Precision targeting of PTENP1-miRNA mediated regulation of PTEN may present as a viable alternative therapy.

Tripathi, A, Zalogina, A, Liao, J, Wurdack, M, Estrecho, E, Zhou, J, Jin, D, Kruk, SS & Kivshar, Y 2023, 'Metasurface-Controlled Photonic Rashba Effect for Upconversion Photoluminescence', Nano Letters, vol. 23, no. 6, pp. 2228-2232.
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Tu, J, Li, W, Hansbro, PM, Yan, Q, Bai, X, Donovan, C, Kim, RY, Galvao, I, Das, A, Yang, C, Zou, J & Diwan, A 2023, 'Smoking and tetramer tryptase accelerate intervertebral disc degeneration by inducing METTL14-mediated DIXDC1 m6 modification', Molecular Therapy, vol. 31, no. 8, pp. 2524-2542.
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Although cigarette smoking (CS) and low back pain (LBP) are common worldwide, their correlations and the mechanisms of action remain unclear. We have shown that excessive activation of mast cells (MCs) and their proteases play key roles in CS-associated diseases, like asthma, chronic obstructive pulmonary disease (COPD), blood coagulation, and lung cancer. Previous studies have also shown that MCs and their proteases induce degenerative musculoskeletal disease. By using a custom-designed smoke-exposure mouse system, we demonstrated that CS results in intervertebral disc (IVD) degeneration and release of MC-restricted tetramer tryptases (TTs) in the IVDs. TTs were found to regulate the expression of methyltransferase 14 (METTL14) at the epigenetic level by inducing N6-methyladenosine (m6A) deposition in the 3' untranslated region (UTR) of the transcript that encodes dishevelled-axin (DIX) domain-containing 1 (DIXDC1). That reaction increases the mRNA stability and expression of Dixdc1. DIXDC1 functionally interacts with disrupted in schizophrenia 1 (DISC1) to accelerate the degeneration and senescence of nucleus pulposus (NP) cells by activating a canonical Wnt pathway. Our study demonstrates the association between CS, MC-derived TTs, and LBP. These findings raise the possibility that METTL14-medicated DIXDC1 m6A modification could serve as a potential therapeutic target to block the development of degeneration of the NP in LBP patients.

Tu, L, Wu, K, Luo, Y, Wang, E, Yuan, J, Zuo, J, Zhou, D, Li, B, Zhou, J, Jin, D & Zhang, H 2023, 'Significant Enhancement of the Upconversion Emission in Highly Er³⁺‐Doped Nanoparticles at Cryogenic Temperatures', Angewandte Chemie, vol. 135, no. 7.
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AbstractRelatively low efficiency is the bottleneck for the application of lanthanide‐doped upconversion nanoparticles (UCNPs). The high‐level doping strategy realized in recent years has not improved the efficiency as much as expected. It is argued that cross relaxation (CR) is not detrimental to upconversion. Here we combine theoretical simulation and spectroscopy to elucidate the role of CR in upconversion process of Er3+ highly doped (HD) UCNPs. It is found that if CR is purposively suppressed, upconversion efficiency can be significantly improved. Specifically, we demonstrate experimentally that inhibition of CR by introducing cryogenic environment (40 K) enhances upconversion emission by more than two orders of magnitude. This work not only elucidates the nature of CR and its non‐negligible adverse effects, but also provides a new perspective for improving upconversion efficiency. The result can be directly applied to cryogenic imaging and wide range temperature sensing.

Tu, L, Wu, K, Luo, Y, Wang, E, Yuan, J, Zuo, J, Zhou, D, Li, B, Zhou, J, Jin, D & Zhang, H 2023, 'Significant Enhancement of the Upconversion Emission in Highly Er³⁺‐Doped Nanoparticles at Cryogenic Temperatures', Angewandte Chemie International Edition, vol. 62, no. 7.
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AbstractRelatively low efficiency is the bottleneck for the application of lanthanide‐doped upconversion nanoparticles (UCNPs). The high‐level doping strategy realized in recent years has not improved the efficiency as much as expected. It is argued that cross relaxation (CR) is not detrimental to upconversion. Here we combine theoretical simulation and spectroscopy to elucidate the role of CR in upconversion process of Er3+ highly doped (HD) UCNPs. It is found that if CR is purposively suppressed, upconversion efficiency can be significantly improved. Specifically, we demonstrate experimentally that inhibition of CR by introducing cryogenic environment (40 K) enhances upconversion emission by more than two orders of magnitude. This work not only elucidates the nature of CR and its non‐negligible adverse effects, but also provides a new perspective for improving upconversion efficiency. The result can be directly applied to cryogenic imaging and wide range temperature sensing.

Tu, X, Gomez, HM, Kim, RY, Brown, AC, de Jong, E, Galvao, I, Faiz, A, Bosco, A, Horvat, JC, Hansbro, P & Donovan, C 2023, 'Airway and parenchyma transcriptomics in a house dust mite model of experimental asthma', Respiratory Research, vol. 24, no. 1, p. 32.
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AbstractLung transcriptomics studies in asthma have provided valuable information in the whole lung context, however, deciphering the individual contributions of the airway and parenchyma in disease pathogenesis may expedite the development of novel targeted treatment strategies. In this study, we performed transcriptomics on the airway and parenchyma using a house dust mite (HDM)-induced model of experimental asthma that replicates key features of the human disease. HDM exposure increased the expression of 3,255 genes, of which 212 were uniquely increased in the airways, 856 uniquely increased in the parenchyma, and 2187 commonly increased in both compartments. Further interrogation of these genes using a combination of network and transcription factor enrichment analyses identified several transcription factors that regulate airway and/or parenchymal gene expression, including transcription factor EC (TFEC), transcription factor PU.1 (SPI1), H2.0-like homeobox (HLX), metal response element binding transcription factor-1 (MTF1) and E74-like factor 4 (ets domain transcription factor, ELF4) involved in controlling innate immune responses. We next assessed the effects of inhibiting lung SPI1 responses using commercially available DB1976 and DB2313 on key disease outcomes. We found that both compounds had no protective effects on airway inflammation, however DB2313 (8 mg/kg) decreased mucus secreting cell number, and both DB2313 (1 mg/kg) and DB1976 (2.5 mg/kg and 1 mg/kg) reduced small airway collagen deposition. Significantly, both compounds decreased airway hyperresponsiveness. This study demonstrates that SPI1 is important in HDM-induced experimental asthma and that its pharmacological inhibition reduces HDM-induced airway collagen deposition and hyperresponsiveness.

Turkmani, S, Bista, S, Wang, JJJ, O’Donnell, AW, Thomson, C, Radcliffe, NJ, Skattebol, J, Redmond, G & Brooks, F 2023, 'Social and Emotional Wellbeing Among Young People; the Mitigating Role of Ecological Domains', Child Indicators Research, vol. 16, no. 3, pp. 941-962.
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AbstractTo examine the role of neighbourhood, what Bronfenbrenner describes as an element in the exosystem, as a protective asset for adolescents’ social and emotional wellbeing. The study used a subset of national data reported by adolescents and their parents from the Longitudinal Study of Australian Children (LSAC). A linear mixed-effect model was used to estimate the association between neighbourhood indicators and trajectories in a measure of social and emotional wellbeing (the SDQ Total Difficulties score) at ages 12–13, 14–15 and 16–17, controlling for age and sex, peer and family relationships and household material resources. The analysis revealed that parents’ perceptions of belonging and their subjective assessments of the condition of housing in the neighbourhood, as well as externally sourced data on neighbourhood accessibility and socio-economic status, were significantly associated with adolescents’ total difficulties scores over time. The findings revealed the role of neighbourhood level protective assets as a potential influence on adolescents’ social and emotional wellbeing. Greater attention should be given to understanding the complex interactions between the resources mobilised by individuals and their families, and the influence of wider environments and social structures on young people’s social and emotional wellbeing.

Turpin, GA, Nelson, A, Holt, SA, Giles, LW, Milogrodzka, I, Horn, RG, Tabor, RF & Hag, LV 2023, 'Investigating Adsorption of Cellulose Nanocrystals at Air–Liquid and Substrate–Liquid Interfaces after pH Manipulation', Advanced Materials Interfaces, vol. 10, no. 11.
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AbstractCoatings of anisotropic nanoparticles such as cellulose nanocrystals (CNCs) can provide tuneable physicochemical surface properties to a substrate such as modifying wettability. These coatings are often formed using dip coating, with CNCs enriched at the air–water interface transferred to a substrate as a monolayer. This process is commonly facilitated by surfactants, which can remain present in the final product, affecting coating properties. In this work, an “additive free” method for creating CNC coatings by exploiting electrostatic interactions within the pH window between pH 2–4 is demonstrated. Within this pH window, the air–water interface is positively charged and CNCs are negatively charged, with surface pressure tensiometry, X‐ray reflectivity, and Brewster angle microscopy indicating that CNCs are driven to the air–water interface. The optimal condition for monolayer coverage was pH 3; at pH 2 charge screening causes localized flocculation at the air–water interface, and at pH 4 interparticle repulsion leads to incomplete, patchy coverage. These findings successfully translate to dip coated CNC monolayers as characterized by atomic force microscopy, showing that the manipulation of pH can facilitate the surfactant‐free dip coating of CNCs, with advantages over the surfactants that are more typically used.

Ung, AT & Asmara, AP 2023, 'Bioactive Phytochemicals of Acacia saligna', Molecules, vol. 28, no. 11, pp. 4396-4396.
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Acacia saligna is native to Western Australia. It has become an introduced and fast-growing plant in other parts of the world due to its ability to adapt to drought, saline and alkaline soils, and hast growing environments. Studies on the bioactivities and phytochemicals of the plant extracts were conducted. However, comprehensive information that links those bioactivities to the identified compounds in the plant’s extracts is still lacking. Data gathered in this review revealed a rich chemical diversity of hydroxybenzoic acids, cinnamic acids, flavonoids, saponins, and pinitols in A. saligna growing in Egypt, Saudi Arabia, Tunisia, South Africa, and Australia. The variability in phytochemical composition and quantity could be attributed to plant parts, growing locations, extraction solvents, and analysis methods. Identified phytochemicals support observed biological activities such as antioxidant, antimicrobial, anticancer, α-glucosidase inhibition, and anti-inflammation in the extracts. The knowledge of chemical structures, biological activities, and possible mechanisms of action of the bioactive phytochemicals identified in A. saligna were discussed. In addition, the structure–activity relationships of dominant active compounds were examined to explain the bioactivities exerted by A. saligna extracts. The review provides valuable insights towards future research and the development of new therapeutics from this plant.

Ungolo, F, Garces, LP, Sherris, M & Zhou, Y 2023, 'Estimation, Comparison and Projection of Multi-factor Age-Cohort Affine Mortality Models'.

Van Eeckhoutte, HP, Donovan, C, Kim, RY, Conlon, TM, Ansari, M, Khan, H, Jayaraman, R, Hansbro, NG, Dondelinger, Y, Delanghe, T, Beal, AM, Geddes, B, Bertin, J, Vanden Berghe, T, De Volder, J, Maes, T, Vandenabeele, P, Vanaudenaerde, BM, Deforce, D, Škevin, S, Van Nieuwerburgh, F, Verhamme, FM, Joos, GF, Idrees, S, Schiller, HB, Yildirim, AÖ, Faiz, A, Bertrand, MJM, Brusselle, GG, Hansbro, PM & Bracke, KR 2023, 'RIPK1 kinase-dependent inflammation and cell death contribute to the pathogenesis of COPD', European Respiratory Journal, vol. 61, no. 4, pp. 2201506-2201506.
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BackgroundReceptor-interacting protein kinase 1 (RIPK1) is a key mediator of regulated cell death (including apoptosis and necroptosis) and inflammation, both drivers of COPD pathogenesis. We aimed to define the contribution of RIPK1 kinase-dependent cell death and inflammation in the pathogenesis of COPD.MethodsWe assessedRIPK1expression in single-cell RNA sequencing (RNA-seq) data from human and mouse lungs, and validated RIPK1 levels in lung tissue of COPD patientsviaimmunohistochemistry. Next, we assessed the consequences of genetic and pharmacological inhibition of RIPK1 kinase activity in experimental COPD, usingRipk1S25D/S25Dkinase-deficient mice and the RIPK1 kinase inhibitor GSK′547.ResultsRIPK1expression increased in alveolar type 1 (AT1), AT2, ciliated and neuroendocrine cells in human COPD. RIPK1 protein levels were significantly increased in airway epithelium of COPD patients compared with never-smokers and smokers without airflow limitation. In mice, exposure to cigarette smoke (CS) increasedRipk1expression similarly in AT2 cells, and further in alveolar macrophages and T-cells. Genetic and/or pharmacological inhibition of RIPK1 kinase activity significantly attenuated airway inflammation upon acute and subacute CS exposure, as well as airway remodelling, emphysema, and apoptotic and necroptotic cell death upon chronic CS exposure. Similarly, pharmacological RIPK1 kinase inhibition significantly attenuated elastase-induced emphysema and lung function decline. Finally, RNA-seq on lung tissue of CS-exposed mice revealed downregulation of cell death and inflammatory pathways upon pharmacological RIPK1 kinase inhibition.

van Nijnatten, J, Faiz, A, Timens, W, Guryev, V, Slebos, D-J, Klooster, K, Hartman, JE, Kole, T, Choy, DF, Chakrabarti, A, Grimbaldeston, M, Rosenberger, CM, Kerstjens, H, Brandsma, C-A & van den Berge, M 2023, 'A bronchial gene signature specific for severe COPD that is retained in the nose', ERJ Open Research, vol. 9, no. 6, pp. 00354-2023.
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IntroductionA subset of COPD patients develops advanced disease with severe airflow obstruction, hyperinflation and extensive emphysema. We propose that the pathogenesis in these patients differs from mild–moderate COPD and is reflected by bronchial gene expression. The aim of the present study was to identify a unique bronchial epithelial gene signature for severe COPD patients.MethodsWe obtained RNA sequencing data from bronchial brushes from 123 ex-smokers with severe COPD, 23 with mild–moderate COPD and 23 non-COPD controls. We identified genes specific to severe COPD by comparing severe COPD to non-COPD controls, followed by removing genes that were also differentially expressed between mild–moderate COPD and non-COPD controls. Next, we performed a pathway analysis on these genes and evaluated whether this signature is retained in matched nasal brushings.ResultsWe identified 219 genes uniquely differentially expressed in severe COPD. Interaction network analysis identifiedVEGFAandFN1as the key genes with the most interactions. Genes were involved in extracellular matrix regulation, collagen binding and the immune response. Of interest were 10 genes (VEGFA,DCN,SPARC,COL6A2,MGP,CYR61,ANXA6,LGALS1,C1QAandC1QB) directly connected to fibronectin 1 (FN1). Most of these genes were lower expressed in severe COPD and showed the same effect in nasal brushings.ConclusionsWe found a uniqu...

van Oppen, MJH & Raina, J 2023, 'Coral holobiont research needs spatial analyses at the microbial scale', Environmental Microbiology, vol. 25, no. 1, pp. 179-183.
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Vanders, RL, Gomez, HM, Hsu, AC, Daly, K, Wark, PAB, Horvat, JC & Hansbro, PM 2023, 'Inflammatory and antiviral responses to influenza A virus infection are dysregulated in pregnant mice with allergic airway disease', American Journal of Physiology-Lung Cellular and Molecular Physiology, vol. 325, no. 3, pp. L385-L398.
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Influenza A virus (IAV) infection during pregnancy with asthma is a major health concern leading to increased morbidity for both mother and baby. Using murine models, we show that IAV infection in pregnancy with allergic airway disease is associated with impaired global antiviral and antimicrobial responses, increased lung inflammation, mucus hypersecretion, and airway hyperresponsiveness (AHR). Targeting specific β-defensins or microRNAs (miRNAs) may prove useful in future treatments for IAV infection during pregnancy.

Verma, A, Hoppenrath, M, Smith, KF, Murray, JS, Harwood, DT, Hosking, JM, Rongo, T, Rhodes, LL & Murray, SA 2023, 'Ostreopsis Schmidt and Coolia Meunier (Dinophyceae, Gonyaulacales) from Cook Islands and Niue (South Pacific Ocean), including description of Ostreopsis tairoto sp. nov.', Scientific Reports, vol. 13, no. 1, pp. 3110-3110.
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AbstractIt is important to decipher the diversity and distribution of benthic dinoflagellates, as there are many morphologically indistinct taxa that differ from one another in production of potent toxins. To date, the genusOstreopsiscomprises twelve described species, of which seven are potentially toxic and produce compounds presenting a threat to human and environmental health. In this study, isolates previously identified as “Ostreopsissp. 3” were sampled from the area where it was first reported, Rarotonga, Cook Islands, and have been taxonomically and phylogenetically characterised asOstreopsis tairotosp. nov. Phylogenetically, the species is closely related to “Ostreopsissp. 8”,O. mascarenensis, “O. sp. 4”,O. fattorussoi, O. rhodesiaeandO. cf.siamensis. Previously, it was considered a part of theO. cf.ovatacomplex but can be distinguished fromO. cf.ovatabased on the small pores identified on this study, and fromO. fattorussoiandO. rhodesiaebased on relative lengths of the 2′ plates. No known palytoxin -like compounds were detected in strains investigated in this study. Strains ofO. lenticularis, Coolia malayensisandC. tropicaliswere also identified and described. This study advances our knowledge of biogeography, distribution, and toxins ofOstreopsisandCooliaspecies.

Violi, JP, Pu, L, Pravadali-Cekic, S, Bishop, DP, Phillips, CR & Rodgers, KJ 2023, 'Effects of the Toxic Non-Protein Amino Acid β-Methylamino-L-Alanine (BMAA) on Intracellular Amino Acid Levels in Neuroblastoma Cells', Toxins, vol. 15, no. 11, pp. 647-647.
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The cyanobacterial non-protein amino acid (AA) β-Methylamino-L-alanine (BMAA) is considered to be a neurotoxin. BMAA caused histopathological changes in brains and spinal cords of primates consistent with some of those seen in early motor neuron disease; however, supplementation with L-serine protected against some of those changes. We examined the impact of BMAA on AA concentrations in human neuroblastoma cells in vitro. Cells were treated with 1000 µM BMAA and intracellular free AA concentrations in treated and control cells were compared at six time-points over a 48 h culture period. BMAA had a profound effect on intracellular AA levels at specific time points but in most cases, AA homeostasis was re-established in the cell. The most heavily impacted amino acid was serine which was depleted in BMAA-treated cells from 9 h onwards. Correction of serine depletion could be a factor in the observation that supplementation with L-serine protects against BMAA toxicity in vitro and in vivo. AAs that could potentially be involved in protection against BMAA-induced oxidation such as histidine, tyrosine, and phenylalanine were depleted in cells at later time points.

Vlaanderen, EJ, Ghaly, TM, Moore, LR, Focardi, A, Paulsen, IT & Tetu, SG 2023, 'Plastic leachate exposure drives antibiotic resistance and virulence in marine bacterial communities', Environmental Pollution, vol. 327, pp. 121558-121558.
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Vo, PHN, Buckley, T, Xu, X, Nguyen, TMH, Rudolph, V & Shukla, P 2023, 'Foam fractionation of per- and polyfluoroalkyl substances (PFASs) in landfill leachate using different cosurfactants', Chemosphere, vol. 310, pp. 136869-136869.
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Vo, PHN, Hamilton, BR, Wepf, RA, Key, TA, Nguyen, TMH, Thai, PK, Thomas, K & Mueller, JF 2023, 'Visualization of the Distribution of PFOS and PFHxS in Concrete by DESI MSI', Environmental Science & Technology Letters, vol. 10, no. 5, pp. 446-451.
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Vo, PHN, Key, TA, Le, TH, McDonough, JT, Porman, S, Fiorenza, S, Nguyen, HTM, Dao, VTN, Mueller, JF & Thai, PK 2023, 'Evaluation of sealants to mitigate the release of per- and polyfluoroalkyl substances (PFAS) from AFFF-impacted concrete: Characterization and forecasting', Water Research X, vol. 20, pp. 100195-100195.
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Vo, PHN, Tscharke, B, Toft, S, Madsen, C, Nguyen, KQ, Nguyen, HTM, Bui, XT, Li, J & Thai, PK 2023, 'Spatiotemporal trends and impact of Covid-19 lockdown on eight sewage contaminants in Brisbane, Australia, from 2012 to 2020', Chemosphere, vol. 314, pp. 137702-137702.
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Vyas, HKN, Xia, B, Alam, D, Gracie, NP, Rothwell, JG, Rice, SA, Carter, D, Cullen, PJ & Mai-Prochnow, A 2023, 'Plasma activated water as a pre-treatment strategy in the context of biofilm-infected chronic wounds', Biofilm, vol. 6, pp. 100154-100154.
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Wade, SA, Webb, JS, Eckert, RB, Jenneman, GE, Rice, SA, Skovhus, TL, Sturman, P, Kotu, SP, Richardson, M & Goeres, DM 2023, 'The role of standards in biofilm research and industry innovation', International Biodeterioration & Biodegradation, vol. 177, pp. 105532-105532.
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Wajahat, M, Kouzani, AZ, Khoo, SY & Mahmud, MAP 2023, 'Comparative study and multi-parameter analysis to optimize device structure of triboelectric nanogenerators', Nanotechnology, vol. 34, no. 42, pp. 425403-425403.
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Abstract Triboelectric nanogenerator is becoming one of the most efficient energy harvesting device among all mechanical energy harvesters. This device consists of dielectric friction layers and metal electrode which generates electrical charges using electrostatic induction effect. There are several factors influencing the performance of this generator which needs to be evaluated prior to experiment. The absence of a universal technique for TENG simulation makes the device design and optimization hard before practical fabrication, which also lengthens the exploration and advancement cycle and hinders the arrival of practical applications. In order to deepen the understanding the core physic behind the working process of this device, this work will provide comparative analysis on different modes of TENG. Systematic investigation on different material combination, effect of material thickness, dielectric constant and impact of surface patterning is evaluated to shortlist the best material combination. COMSOL Multiphysics simulating environment is used to design, model and analyze factor affecting the overall output performance of TENG. The stationary study in this simulator is performed using 2D geometry structure with higher mesh density. During this study short circuit and open circuit condition were applied to observe the behavior of charge and electric potential produced. This observation is analyzed by plotting charge transfer/electric potential against various displacement distances of dielectric friction layers. The ouput is then provided to load ciruitary to measure the maximum output power of the models. Overall, this study provides an excellent understanding and multi-parameter analysis on basic theoretical and simulation modeling of TENG device.

Walworth, NG, Espinoza, JL, Argyle, PA, Hinners, J, Levine, NM, Doblin, MA, Dupont, CL & Collins, S 2023, 'Genus-Wide Transcriptional Landscapes Reveal Correlated Gene Networks Underlying Microevolutionary Divergence in Diatoms', Molecular Biology and Evolution, vol. 40, no. 10.
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Abstract Marine microbes like diatoms make up the base of marine food webs and drive global nutrient cycles. Despite their key roles in ecology, biogeochemistry, and biotechnology, we have limited empirical data on how forces other than adaptation may drive diatom diversification, especially in the absence of environmental change. One key feature of diatom populations is frequent extreme reductions in population size, which can occur both in situ and ex situ as part of bloom-and-bust growth dynamics. This can drive divergence between closely related lineages, even in the absence of environmental differences. Here, we combine experimental evolution and transcriptome landscapes (t-scapes) to reveal repeated evolutionary divergence within several species of diatoms in a constant environment. We show that most of the transcriptional divergence can be captured on a reduced set of axes, and that repeatable evolution can occur along a single major axis of variation defined by core ortholog expression comprising common metabolic pathways. Previous work has associated specific transcriptional changes in gene networks with environmental factors. Here, we find that these same gene networks diverge in the absence of environmental change, suggesting these pathways may be central in generating phenotypic diversity as a result of both selective and random evolutionary forces. If this is the case, these genes and the functions they encode may represent universal axes of variation. Such axes that capture suites of interacting transcriptional changes during diversification improve our understanding of both global patterns in local adaptation and microdiversity, as well as evolutionary forces shaping algal cultivation.

Wang, CY, Wang, J, Zhang, L, Zhang, SW, Wang, L, Zhao, SZ, Chen, ZH, Zhang, X, Xie, M, Wang, T, Chen-Yu Hsu, A, Qin, L, Oliver, BG, Liu, L, Wan, HJ, Liu, D, Luo, FM, Li, WM & Wang, G 2023, 'Self-Reported Insufficient Sleep Is Associated With Clinical and Inflammatory Features of Asthma: A Prospective Cohort Study', The Journal of Allergy and Clinical Immunology: In Practice, vol. 11, no. 4, pp. 1200-1210.e4.
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Wang, D, Wang, Y, Di, X, Wang, F, Wanninayaka, A, Carnell, M, Hardeman, EC, Jin, D & Gunning, PW 2023, 'Cortical tension drug screen links mitotic spindle integrity to Rho pathway', Current Biology, vol. 33, no. 20, pp. 4458-4469.e4.
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Wang, F, Pasin, D, Skinnider, MA, Liigand, J, Kleis, J-N, Brown, D, Oler, E, Sajed, T, Gautam, V, Harrison, S, Greiner, R, Foster, LJ, Dalsgaard, PW & Wishart, DS 2023, 'Deep Learning-Enabled MS/MS Spectrum Prediction Facilitates Automated Identification Of Novel Psychoactive Substances', Analytical Chemistry, vol. 95, no. 50, pp. 18326-18334.
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The market for illicit drugs has been reshaped by the emergence of more than 1100 new psychoactive substances (NPS) over the past decade, posing a major challenge to the forensic and toxicological laboratories tasked with detecting and identifying them. Tandem mass spectrometry (MS/MS) is the primary method used to screen for NPS within seized materials or biological samples. The most contemporary workflows necessitate labor-intensive and expensive MS/MS reference standards, which may not be available for recently emerged NPS on the illicit market. Here, we present NPS-MS, a deep learning method capable of accurately predicting the MS/MS spectra of known and hypothesized NPS from their chemical structures alone. NPS-MS is trained by transfer learning from a generic MS/MS prediction model on a large data set of MS/MS spectra. We show that this approach enables a more accurate identification of NPS from experimentally acquired MS/MS spectra than any existing method. We demonstrate the application of NPS-MS to identify a novel derivative of phencyclidine (PCP) within an unknown powder seized in Denmark without the use of any reference standards. We anticipate that NPS-MS will allow forensic laboratories to identify more rapidly both known and newly emerging NPS. NPS-MS is available as a web server at https://nps-ms.ca/, which provides MS/MS spectra prediction capabilities for given NPS compounds. Additionally, it offers MS/MS spectra identification against a vast database comprising approximately 8.7 million predicted NPS compounds from DarkNPS and 24.5 million predicted ESI-QToF-MS/MS spectra for these compounds.

Wang, J, Song, G, Liddell, M, Morellato, P, Lee, CKF, Yang, D, Alberton, B, Detto, M, Ma, X, Zhao, Y, Yeung, HCH, Zhang, H, Ng, M, Nelson, BW, Huete, A & Wu, J 2023, 'An ecologically-constrained deep learning model for tropical leaf phenology monitoring using PlanetScope satellites', Remote Sensing of Environment, vol. 286, pp. 113429-113429.
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Wang, J, Zhang, X, Zhang, L, Liu, Y, Wang, G, Zhang, HP, Wang, L, Kang, DY, Oliver, BG, Wan, HJ, McDonald, VM, Chen-Yu Hsu, A, Liu, D, Li, WM, Birring, SS & Wang, G 2023, 'Age-Related Clinical Characteristics, Inflammatory Features, Phenotypes, and Treatment Response in Asthma', The Journal of Allergy and Clinical Immunology: In Practice, vol. 11, no. 1, pp. 210-219.e3.
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Wang, JJJ & Chan, JSK 2023, 'Stochastic modelling of volatility and inter-relationships in the Australian electricity markets', Communications in Statistics - Simulation and Computation, vol. 52, no. 8, pp. 3877-3896.
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Wang, L, Wang, R, Zheng, Q, Yao, X, Zhang, C, Fu, S, Wei, Z, Yun, K & Guo, Z 2023, 'Simulating dynamic interaction between diazepam and ethanol targeting the GABAA receptor via in silico model', NeuroToxicology, vol. 95, pp. 136-143.
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Wang, T, Gu, W, Yu, L, Guo, X, Yang, J, Sun, X, Guan, J, Zhou, L, Wang, C, Yao, H, Zhang, X & Wang, G 2023, 'MXene: An efficient hemoperfusion sorbent for the removal of uremic toxins', Journal of Materiomics, vol. 9, no. 6, pp. 1129-1140.
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Wang, X, Ye, R, Duyar, MS, Price, CAH, Tian, H, Chen, Y, Ta, N, Liu, H & Liu, J 2023, 'Design of mesoporous ZnCoSiOx hollow nanoreactors with specific spatial distribution of metal species for selective CO2 hydrogenation', Nano Research, vol. 16, no. 4, pp. 5601-5609.
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In heterogeneous catalysis, the precise placement of active components to perform unique functions in cooperation with each other is a tremendous challenge. The migration of matter on micro/nano-scale caused by diffusion is a promising pathway for design of catalytic nanoreactors with precise active sites location and controllable microenvironment through compartmentalization and confinement effects. Herein, we report two categories of mesoporous ZnCoSiOx hollow nanoreactors with different metal distributions and microenvironment engineered by the diffusion behavior of metal species in confined nanospace. Double-shelled hollow structures with well-distributed metal species were obtained by adopting core@shell structured ZnCo-zeolitic imidazolate framework (ZIF)@SiO2 as a template and employing three stages of hydrothermal treatment including the decomposition of ZIF, diffusion of metal species into the silica shell, and Ostwald ripening. Additionally, the formation of yolk@shell structure with a collective (Zn-Co) metal oxide as the yolk was achieved by direct pyrolysis of ZnCo-ZIF@SiO2. In CO2 hydrogenation, ZnCoSiOx with double-shelled hollow structures and yolk@shell structures respectively afford CO and CH4 as main product, which is related with different dispersion and location of active sites in the two catalysts. This study provides an efficient method for the synthesis of catalytic nanoreactors on the basis of insights of the atomic diffusion in confined space at the mesoscale. [Figure not available: see fulltext.].

Wang, Y, Huang, X, Li, F, Jia, X, Jia, N, Fu, J, Liu, S, Zhang, J, Ge, H, Huang, S, Hui, Y, Sun, C, Xiao, F, Cui, X, Luu, LDW, Qu, D, Li, J & Tai, J 2023, 'Serum-integrated omics reveal the host response landscape for severe pediatric community-acquired pneumonia', Critical Care, vol. 27, no. 1, p. 79.
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Abstract Objective Community-acquired pneumonia (CAP) is the primary cause of death for children under five years of age globally. Hence, it is essential to investigate new early biomarkers and potential mechanisms involved in disease severity. Methods Proteomics combined with metabolomics was performed to identify biomarkers suitable for early diagnosis of severe CAP. In the training cohort, proteomics and metabolomics were performed on serum samples obtained from 20 severe CAPs (S-CAPs), 15 non-severe CAPs (NS-CAPs) and 15 healthy controls (CONs). In the verification cohort, selected biomarkers and their combinations were validated using ELISA and metabolomics in an independent cohort of 129 subjects. Finally, a combined proteomics and metabolomics analysis was performed to understand the major pathological features and reasons for severity of CAP. Results The proteomic and metabolic signature was markedly different between S-CAPs, NS-CAPs and CONs. A new serum biomarker panel including 2 proteins [C-reactive protein (CRP), lipopolysaccharide (LBP)] and 3 metabolites [Fasciculol C, PE (14:0/16:1(19Z)), PS (20:0/22:6(4Z, 7Z, 10Z, 13Z, 16Z, 19Z))] was developed to identify CAP and to distinguish severe pneumonia. Pathway analysis of changes revealed activation of the cell death pathway, a dysregulated complement system, coagulation cascade and platelet function, and the inflammatory responses as contributors to tissue damage in children with CAP. Additionally, activation of glycolysis and higher levels of nucleotides led to imbalanced deoxyribonucleotide pools contributing to the development of severe CAP. Finally, dysregulated lipid meta...

Wang, Y, Ninaber, DK, Faiz, A, van der Linden, AC, van Schadewijk, A, Lutter, R, Hiemstra, PS, van der Does, AM & Ravi, A 2023, 'Acute cigarette smoke exposure leads to higher viral infection in human bronchial epithelial cultures by altering interferon, glycolysis and GDF15-related pathways', Respiratory Research, vol. 24, no. 1, p. 207.
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Abstract Background Acute exacerbations of chronic inflammatory lung diseases, such as chronic obstructive pulmonary disease (COPD), are frequently associated with rhinovirus (RV) infections. Despite these associations, the pathogenesis of virus-induced exacerbations is incompletely understood. We aimed to investigate effects of cigarette smoke (CS), a primary risk factor for COPD, on RV infection in airway epithelium and identify novel mechanisms related to these effects. Methods Primary bronchial epithelial cells (PBEC) from COPD patients and controls were differentiated by culture at the air–liquid interface (ALI) and exposed to CS and RV-A16. Bulk RNA sequencing was performed using samples collected at 6 and 24 h post infection (hpi), and viral load, mediator and l-lactate levels were measured at 6, 24 and 48hpi. To further delineate the effect of CS on RV-A16 infection, we performed growth differentiation factor 15 (GDF15) knockdown, l-lactate and interferon pre-treatment in ALI-PBEC. We performed deconvolution analysis to predict changes in the cell composition of ALI-PBEC after the various exposures. Finally, we compared transcriptional responses of ALI-PBEC to those in nasal epithelium after human RV-A16 challenge. Results CS exposure impaired antiviral responses at 6hpi and increased viral replication at 24 and 48hpi in ALI-PBEC. At 24hpi, CS exposure enhanced expression of RV-A16-induced epithelial interferons, inflammation-related genes and CXCL8. CS exposure increased expression of oxidative stress-related genes, of GDF15, and decreased mitochondrial membrane potential. GDF15<...

Wang, Y, Sun, Q, Zhang, Y, Li, X, Liang, Q, Guo, R, Zhang, L, Han, X, Wang, J, Shao, L, Xue, Y, Yang, Y, Li, H, Nie, L, Shi, W, Liu, Q, Zhang, J, Duan, H, Huang, H, Luu, LDW, Tai, J, Yang, X & Wang, G 2023, 'Systemic immune dysregulation in severe tuberculosis patients revealed by a single-cell transcriptome atlas', Journal of Infection, vol. 86, no. 5, pp. 421-438.
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Wang, Y, Wang, X, Jia, X, Li, J, Fu, J, Huang, X, Cui, X, Wang, B, Luo, W, Lin, C, Li, Z, Luu, LDW, Li, S, Zhu, X & Tai, J 2023, 'Influenza vaccination features revealed by a single‐cell transcriptome atlas', Journal of Medical Virology, vol. 95, no. 1.
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AbstractEmerging and re‐emerging viruses like influenza virus pose a continuous global public health threat. Vaccines are one of the most effective public health strategies for controlling infectious diseases. However, little is known about the immunological features of vaccination at the single‐cell resolution, including for influenza vaccination. Here, we report the single‐cell transcriptome atlas of longitudinally collected peripheral blood mononuclear cells (PBMCs) in individuals immunized with an inactivated influenza vaccine. Overall, vaccination with the influenza vaccine only had a small impact on the composition of peripheral immune cells, but elicited global transcriptional changes in multiple immune cell subsets. In plasma and B cell subsets, transcriptomic changes, which were mostly involved in antibody production as well as B cell activation and differentiation, were observed after influenza vaccinations. In influenza‐vaccinated individuals, we found a reduction in multiple biological processes (e.g., interferon response, inflammatory response, HLA‐I/II molecules, cellular apoptosis, migration, and cytotoxicity, etc.,) 7 days postvaccination in multiple immune cell subsets. However, 14 days postvaccination, these levels returned to similar levels observed in prevaccination samples. Additionally, we did not observe significant upregulation of pro‐inflammatory response genes and key thrombosis‐related genes in influenza‐vaccinated individuals. Taken together, we report a cell atlas of the peripheral immune response to influenza vaccination and provide a resource for understanding the immunological response mechanisms of influenza vaccination.

Watherston, J & McNevin, D 2023, 'Skull and long bones – Forensic DNA techniques for historic shipwreck human remains', Australian Journal of Forensic Sciences, vol. ahead-of-print, no. ahead-of-print, pp. 1-25.
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Human remains have been recovered from a number of historic shipwrecks and their associated sites, often hundreds of years post-mortem. While remains of victims who have fled following wrecking can be subject to a range of environmental exposures, human remains in marine environments are subject to unique decomposition processes, faunal predation and impacts on DNA. Researchers in museums and academic institutions holding historic shipwreck remains have applied a plethora of scientific testing methods to extract information from artefacts and shipwreck remains. Specialist forensic DNA techniques, often adapted from ancient and archaeological DNA methods, are designed to maximize DNA recovery, and advances in technology and forensic biology have increased options for genotyping compromised human skeletal samples. A vast array of new genetic markers can now be targeted for interrogation to reveal externally visible characteristics, biogeographical ancestry or extended genetic relatives of victims. Some of these techniques have already been applied to historic shipwreck remains. This paper reviews current and emerging forensic DNA techniques available for recovering and revealing genetic information from historic shipwreck remains. It aims to direct investigators conducting genetic testing on historic shipwreck human remains to forensic DNA techniques as a possible approach for yielding further invaluable information.

Webb, JK, Jolly, CJ, Hinds, M, Adams, C, Cuartas‐Villa, S, Lapwong, Y & Letnic, M 2023, 'Effects of the Australian 2019–2020 megafires on a population of endangered broad‐headed snakes Hoplocephalus bungaroides', Austral Ecology, vol. 48, no. 1, pp. 24-30.
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AbstractThe 2019–2020 Australian megafires were unprecedented in their intensity and extent. These wildfires may have caused high mortality of adult broad‐headed snakes Hoplocephalus bungaroides which shelter inside tree hollows during summer. We evaluated the impacts of two high‐intensity wildfires (2002 Touga Fire and 2020 Morton Fire) on a broad‐headed snake population in Morton National Park, south‐eastern Australia. We analysed a 29‐year mark–recapture data set to estimate survival rates of adults in years with and without wildfires, and with and without human disturbance to rock outcrops. To examine the short‐term effects of fire on occupancy, we analysed presence–absence data collected from 25 sites during 2019 and 2020. Estimates of occupancy were higher for 2020 (0.93 ± 0.09) than for 2019 (0.66 ± 0.14), while detection rates were constant (0.40 ± 0.06). Over the period 1992–2020, the best supported Cormack–Jolly–Seber model was one in which adult survival rates were high and stable (0.81 ± 0.04), but were 23% lower in years when humans disturbed rocks (0.63 ± 0.08). A model in which adult mortality was 20% higher in years with human disturbance and 14% higher in years with wildfires was also supported. Estimates of abundance revealed that the population declined by 34% after the Touga Fire, and 26% after the Morton Fire. Over the 29‐year study, the population has declined by 60%. Our results highlight how mortality events from wildfires need to be evaluated in the context of other threatening processes. For this population, the removal of snakes and associated habitat disturbance poses a more serious threat to population viability than infrequent wildfires.

Webster, J, Dadd‐Daigle, P, Chapman, TA & Kirkby, K 2023, 'Investigating the defoliating‐like (DL) VCG2A pathotype of Verticillium dahliae through identification and prediction of secreted proteins from genomes of Australian isolates', Plant Pathology, vol. 72, no. 2, pp. 334-341.
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AbstractIn Australia, recent investigations have reported the presence of a number of Verticillium dahliae pathotypes (VCG1A, VCG2A and VCG6) that cause disease in cotton and agricultural weeds. During these investigations, it was observed that a VCG2A V. dahliae displayed greater virulence than previously reported in local and international isolates. Genome sequencing of seven V. dahliae isolates was performed using a mixture of short and long reads sequencing technologies. Of these seven isolates, four were identified as D VCG1A, one ND VCG2A, a recently identified Australian VCG6 as well as a virulent VCG2A, classified as “defoliating‐like”. The secreted protein repertoire from the genomes of these Australian V. dahliae isolates was predicted using four separate signal prediction methods. The consensus secreted protein set of the isolates revealed the presence of 20 proteins that were present in all virulent isolates, including the virulent DL VCG2A, and absent in the nonvirulent VCG2A isolates. Ten of these proteins had a functional annotation and were identified as ligninase H8, lipolytic enzyme, laccase, amine oxidase, spherulin‐1A, dipeptidyl‐peptidase, monooxygenase, dienelactone hydrolase, carboxypeptidase and fibronectin by BLASTP.

Wen, C, Kong, M, Gu, Y, Zhang, J, Chen, X, Sun, L-D & Feng, W 2023, 'Thermal-Sensitive Luminescence Dynamics of NaNdF₄:Yb@CaF₂ Nanostructures as Nanothermometers', ACS Applied Nano Materials, vol. 6, no. 11, pp. 9839-9848.
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Westerhausen, MT, Bernard, M, Choi, G, Jeffries-Stokes, C, Chandrajith, R, Banati, R & Bishop, DP 2023, 'Preparation of matrix-matched standards for the analysis of teeth via laser ablation-inductively coupled plasma-mass spectrometry', Analytical Methods, vol. 15, no. 6, pp. 797-806.
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Matrix-matched calibrants improved the detection of toxic metals in teeth.

Westlund, E, Bergenstråle, A, Pokhrel, A, Chan, H, Skoglund, U, Daley, DO & Söderström, B 2023, 'Application of nanotags and nanobodies for live cell single-molecule imaging of the Z-ring in Escherichia coli', Current Genetics, vol. 69, no. 2-3, pp. 153-163.
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AbstractUnderstanding where proteins are localized in a bacterial cell is essential for understanding their function and regulation. This is particularly important for proteins that are involved in cell division, which localize at the division septum and assemble into highly regulated complexes. Current knowledge of these complexes has been greatly facilitated by super-resolution imaging using fluorescent protein fusions. Herein, we demonstrate with FtsZ that single-molecule PALM images can be obtained in-vivo using a genetically fused nanotag (ALFA), and a corresponding nanobody fused to mEos3.2. The methodology presented is applicable to other bacterial proteins.

Weyermann, C, Willis, S, Margot, P & Roux, C 2023, 'Towards more relevance in forensic science research and development', Forensic Science International, vol. 348, pp. 111592-111592.
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Widjaja, M, Kim, RY & Donovan, C 2023, 'Hybridized face‐to‐face and online laboratory content in the time of COVID‐19', Biochemistry and Molecular Biology Education, vol. 51, no. 3, pp. 327-328.
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AbstractThis article describes strategies to adapt and ensure equivalency of content coverage for an existing protein assay laboratory practical for concurrent face‐to‐face and online deliveries during COVID‐19 and beyond.

Winskel-Wood, B, Padula, MP, Marks, DC & Johnson, L 2023, 'The phenotype of cryopreserved platelets influences the formation of platelet-leukocyte aggregates in an in vitro model', Platelets, vol. 34, no. 1.
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Wong, LL, Mugunthan, S, Kundukad, B, Ho, JCS, Rice, SA, Hinks, J, Seviour, T, Parikh, AN & Kjelleberg, S 2023, 'Microbial biofilms are shaped by the constant dialogue between biological and physical forces in the extracellular matrix', Environmental Microbiology, vol. 25, no. 1, pp. 199-208.
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Wong, WW, Wang, N, Esser, BD, Church, SA, Li, L, Lockrey, M, Aharonovich, I, Parkinson, P, Etheridge, J, Jagadish, C & Tan, HH 2023, 'Bottom-up, Chip-Scale Engineering of Low Threshold, Multi-Quantum-Well Microring Lasers', ACS Nano, vol. 17, no. 15, pp. 15065-15076.
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Woodward, H, Moret, S & Chadwick, S 2023, 'Biodegradable plastics and their impact on fingermark detection methods', Forensic Science International, vol. 344, pp. 111571-111571.
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Wu, S, Yang, Z, Ma, C, Zhang, X, Mi, C, Zhou, J, Guo, Z & Jin, D 2023, 'Deep learning enhanced NIR-II volumetric imaging of whole mice vasculature', Opto-Electronic Advances, vol. 6, no. 4, pp. 220105-220105.
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Xia, B, Vyas, HKN, Zhou, R, Zhang, T, Hong, J, Rothwell, JG, Rice, SA, Carter, D, Ostrikov, KK, Cullen, PJ & Mai-Prochnow, A 2023, 'The importance of superoxide anion for Escherichia coli biofilm removal using plasma-activated water', Journal of Environmental Chemical Engineering, vol. 11, no. 3, pp. 109977-109977.
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Xiao, J, Xiao, Y, Li, J, Gong, C, Nie, X, Gao, H, Sun, B, Liu, H & Wang, G 2023, 'Advanced nanoengineering strategies endow high‐performance layered transition‐metal oxide cathodes for sodium‐ion batteries', SmartMat, vol. 4, no. 5.
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AbstractConsidering the abundance and low price of sodium, sodium‐ion batteries (SIBs) have shown great potential as an alternative to existing lithium‐based batteries in large‐scale energy storage systems, including electric automobiles and smart grids. Cathode materials, which largely decide the cost and the electrochemical performance of the full SIBs, have been extensively studied. Among the reported cathodes, layered transition‐metal oxides (LTMOs) are regarded as the most extremely promising candidates for the commercial application of the SIBs owing to their high specific capacity, superior redox potential, and suitable scalable preparation. Nevertheless, irreversible structural evolution, sluggish kinetics, and water sensitivity are still the critical bottlenecks for their practical utilization. Nanoengineering may offer an opportunity to address the above issues by increasing reactivity, shortening diffusion pathways, and strengthening structural stability. Herein, a comprehensive summary of the modification strategies for LTMOs is presented, emphasizing optimizing the structure, restraining detrimental phase transition, and promoting diffusion kinetics. This review intends to facilitate an in‐depth understanding of structure–composition–property correlation and offer guidance to the further development of the LTMO cathodes for next‐generation energy storage systems.

Xie, Q, Moore, CE, Cleverly, J, Hall, CC, Ding, Y, Ma, X, Leigh, A & Huete, A 2023, 'Land surface phenology indicators retrieved across diverse ecosystems using a modified threshold algorithm', Ecological Indicators, vol. 147, pp. 110000-110000.
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Xie, W, Zhang, C, Wang, Z, Chen, H, Gu, T, Zhou, T, Wu, Y, Xia, F, Li, M, Wang, J, Jiao, R, Cui, J & Jin, S 2023, 'ATG4B antagonizes antiviral immunity by GABARAP-directed autophagic degradation of TBK1.', Autophagy, vol. 19, no. 11, pp. 2853-2868.
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Baf A1: bafilomycin A1; GABARAP: GABA type A receptor-associated protein; GFP: green fluorescent protein; IFN: interferon; IKBKE/IKKi: inhibitor of nuclear factor kappa B kinase subunit epsilon; IRF3: interferon regulatory factor 3; ISG: interferon-stimulated gene; ISRE: IFN-stimulated response element; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAVS: mitochondrial antiviral signaling protein; MOI: multiplicity of infection; PAMPs: pathogen-associated molecule patterns; RIGI/DDX58: RNA sensor RIG-I; SeV: Sendai virus; siRNA: small interfering RNA; TBK1: TANK binding kinase 1; WT: wild-type; VSV: vesicular stomatitis virus.

Xie, Y, Chen, X, Sun, K, Zhang, J, Lai, W, Liu, H & Wang, G 2023, 'Direct Oxygen‐Oxygen Cleavage through Optimizing Interatomic Distances in Dual Single‐atom Electrocatalysts for Efficient Oxygen Reduction Reaction', Angewandte Chemie, vol. 135, no. 17.
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AbstractThe oxygen reduction reaction (ORR) on transition single‐atom catalysts (SACs) is sustainable in energy‐conversion devices. However, the atomically controllable fabrication of single‐atom sites and the sluggish kinetics of ORR have remained challenging. Here, we accelerate the kinetics of acid ORR through a direct O−O cleavage pathway through using a bi‐functional ligand‐assisted strategy to pre‐control the distance of hetero‐metal atoms. Concretely, the as‐synthesized Fe−Zn diatomic pairs on carbon substrates exhibited an outstanding ORR performance with the ultrahigh half‐wave potential of 0.86 V vs. RHE in acid electrolyte. Experimental evidence and density functional theory calculations confirmed that the Fe−Zn diatomic pairs with a specific distance range of around 3 Å, which is the key to their ultrahigh activity, average the interaction between hetero‐diatomic active sites and oxygen molecules. This work offers new insight into atomically controllable SACs synthesis and addresses the limitations of the ORR dissociative mechanism.

Xie, Y, Chen, X, Sun, K, Zhang, J, Lai, W, Liu, H & Wang, G 2023, 'Direct Oxygen‐Oxygen Cleavage through Optimizing Interatomic Distances in Dual Single‐atom Electrocatalysts for Efficient Oxygen Reduction Reaction', Angewandte Chemie International Edition, vol. 62, no. 17.
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AbstractThe oxygen reduction reaction (ORR) on transition single‐atom catalysts (SACs) is sustainable in energy‐conversion devices. However, the atomically controllable fabrication of single‐atom sites and the sluggish kinetics of ORR have remained challenging. Here, we accelerate the kinetics of acid ORR through a direct O−O cleavage pathway through using a bi‐functional ligand‐assisted strategy to pre‐control the distance of hetero‐metal atoms. Concretely, the as‐synthesized Fe−Zn diatomic pairs on carbon substrates exhibited an outstanding ORR performance with the ultrahigh half‐wave potential of 0.86 V vs. RHE in acid electrolyte. Experimental evidence and density functional theory calculations confirmed that the Fe−Zn diatomic pairs with a specific distance range of around 3 Å, which is the key to their ultrahigh activity, average the interaction between hetero‐diatomic active sites and oxygen molecules. This work offers new insight into atomically controllable SACs synthesis and addresses the limitations of the ORR dissociative mechanism.

Xirocostas, ZA, Ollerton, J, Tamme, R, Peco, B, Lesieur, V, Slavich, E, Junker, RR, Pärtel, M, Raghu, S, Uesugi, A, Bonser, SP, Chiarenza, GM, Hovenden, MJ & Moles, AT 2023, 'The great escape: patterns of enemy release are not explained by time, space or climate', Proceedings of the Royal Society B: Biological Sciences, vol. 290, no. 2005.
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When a plant is introduced to a new ecosystem it may escape from some of its coevolved herbivores. Reduced herbivore damage, and the ability of introduced plants to allocate resources from defence to growth and reproduction can increase the success of introduced species. This mechanism is known as enemy release and is known to occur in some species and situations, but not in others. Understanding the conditions under which enemy release is most likely to occur is important, as this will help us to identify which species and habitats may be most at risk of invasion. We compared in situ measurements of herbivory on 16 plant species at 12 locations within their native European and introduced Australian ranges to quantify their level of enemy release and understand the relationship between enemy release and time, space and climate. Overall, plants experienced approximately seven times more herbivore damage in their native range than in their introduced range. We found no evidence that enemy release was related to time since introduction, introduced range size, temperature, precipitation, humidity or elevation. From here, we can explore whether traits, such as leaf defences or phylogenetic relatedness to neighbouring plants, are stronger indicators of enemy release across species.

Yaghoubi Naei, V, Bordhan, P, Mirakhorli, F, Khorrami, M, Shrestha, J, Nazari, H, Kulasinghe, A & Ebrahimi Warkiani, M 2023, 'Advances in novel strategies for isolation, characterization, and analysis of CTCs and ctDNA', Therapeutic Advances in Medical Oncology, vol. 15.
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Over the past decade, the detection and analysis of liquid biopsy biomarkers such as circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have advanced significantly. They have received recognition for their clinical usefulness in detecting cancer at an early stage, monitoring disease, and evaluating treatment response. The emergence of liquid biopsy has been a helpful development, as it offers a minimally invasive, rapid, real-time monitoring, and possible alternative to traditional tissue biopsies. In resource-limited settings, the ideal platform for liquid biopsy should not only extract more CTCs or ctDNA from a minimal sample volume but also accurately represent the molecular heterogeneity of the patient’s disease. This review covers novel strategies and advancements in CTC and ctDNA-based liquid biopsy platforms, including microfluidic applications and comprehensive analysis of molecular complexity. We discuss these systems’ operational principles and performance efficiencies, as well as future opportunities and challenges for their implementation in clinical settings. In addition, we emphasize the importance of integrated platforms that incorporate machine learning and artificial intelligence in accurate liquid biopsy detection systems, which can greatly improve cancer management and enable precision diagnostics.

Yamaguchi, A, Hoppenrath, M, Murray, S, Kretzschmar, AL, Horiguchi, T & Wakeman, KC 2023, 'Morphology and molecular phylogeny of the benthic dinoflagellates (Dinophyceae, Peridiniales) Amphidiniopsis crumena n. sp. and Amphidiniopsis nileribanjensis n. sp.', European Journal of Protistology, vol. 87, pp. 125940-125940.
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Yan, G, Sun, X, Zhang, Y, Li, H, Huang, H, Jia, B, Su, D & Ma, T 2023, 'Metal-Free 2D/2D van der Waals Heterojunction Based on Covalent Organic Frameworks for Highly Efficient Solar Energy Catalysis', Nano-Micro Letters, vol. 15, no. 1.
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Abstract Covalent organic frameworks (COFs) have emerged as a kind of rising star materials in photocatalysis. However, their photocatalytic activities are restricted by the high photogenerated electron–hole pairs recombination rate. Herein, a novel metal-free 2D/2D van der Waals heterojunction, composed of a two-dimensional (2D) COF with ketoenamine linkage (TpPa-1-COF) and 2D defective hexagonal boron nitride (h-BN), is successfully constructed through in situ solvothermal method. Benefitting from the presence of VDW heterojunction, larger contact area and intimate electronic coupling can be formed between the interface of TpPa-1-COF and defective h-BN, which make contributions to promoting charge carriers separation. The introduced defects can also endow the h-BN with porous structure, thus providing more reactive sites. Moreover, the TpPa-1-COF will undergo a structural transformation after being integrated with defective h-BN, which can enlarge the gap between the conduction band position of the h-BN and TpPa-1-COF, and suppress electron backflow, corroborated by experimental and density functional theory calculations results. Accordingly, the resulting porous h-BN/TpPa-1-COF metal-free VDW heterojunction displays outstanding solar energy catalytic activity for water splitting without co-catalysts, and the H2 evolution rate can reach up to 3.15 mmol g−1 h−1, which is about 67 times greater than that of pristine TpPa-1-COF, also surpassing that of state-of-the-art metal-free-based photocatalysts reported to date. In particular, it is the first work for constructing COFs-based heterojunctions with the help of h-BN, which may pro...

Yang, J, Guo, X, Gao, H, Wang, T, Liu, Z, Yang, Q, Yao, H, Li, J, Wang, C & Wang, G 2023, 'A High‐Performance Alloy‐Based Anode Enabled by Surface and Interface Engineering for Wide‐Temperature Sodium‐Ion Batteries', Advanced Energy Materials, vol. 13, no. 29.
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AbstractAlloy‐based anodes have shown great potential to be applied in sodium‐ion batteries (SIBs) due to their high theoretical capacities, suitable working potential, and abundant earth reserves. However, their practical applications are severely impeded by large volume expansion, unstable solid‐electrolyte interfaces (SEI), and sluggish reaction kinetics during cycling. Herein, a surface engineering of tin nanorods via N‐doped carbon layers (Sn@NC) and an interface engineering strategy to improve the electrochemical performance in SIBs are reported. In particular, the authors demonstrate that uniform surface modification can effectively facilitate electron and sodium transport kinetics, confine alloy pulverization, and simultaneously synergize interactions with the ether‐based electrolyte to form a robust organic‐inorganic SEI. Moreover, it is discovered that the diethylene glycol dimethyl ether electrolyte with strong stability and an optimized Na+ solvation structure can co‐embed the carbon layer to achieve fast reaction kinetics. Consequently, Sn@NC anodes deliver extra‐long cycling stability of more than 10 000 cycles. The full cell of Na3V2(PO4)3║Sn@NC exhibits high energy density (215 Wh kg−1), excellent high‐rate capability (reaches 80% capacity in 2 min), and long cycle life over a wide temperature range of −20 to 50 °C.

Yang, J, Wang, T, Guo, X, Sheng, X, Li, J, Wang, C & Wang, G 2023, 'Flexible sodium-ion capacitors boosted by high electrochemically-reactive and structurally-stable Sb2S3 nanowire/Ti3C2Tx MXene film anodes', Nano Research, vol. 16, no. 4, pp. 5592-5600.
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Yang, J, Yin, B, Zhang, S, Sun, Y, Li, J, Su, D & Ma, T 2023, 'Macromolecules Promoting Robust Zinc Anode by Synergistic Coordination Effect and Charge Redistribution', Small, vol. 19, no. 45.
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AbstractZn dendrite formation is the main obstacle to commercializing aqueous zinc–ion batteries (ZIBs). α‐cyclodextrin (α‐CD) is proposed as an environmentally friendly macromolecule additive in the ZnSO4‐based electrolyte to obtain stable and reversible Zn anodes. The results show that α‐CD molecules’ unique 3D structure can effectively regulate the mass transfer of the electrolyte components and isolate the Zn anode from H2O molecules. The α‐CD provides abundant electrons to the Zn (002) crystallographic plane, which induces charge density redistribution. Such an effect relieves the reduction and aggregation of Zn2+ cations while protecting the Zn metal anode from water molecules. Finally, a small amount of α‐CD additive (0.01 M) can enhance the performance of Zn significantly in Zn||Cu cells (1980 cycles with 99.45% average CE) and Zn||Zn cells (8000 h ultra‐long cycle life). The excellent practical applicability was further verified in Zn||MnO2 cells.

Yang, L-Y, Yu, R, Wu, J, Zhang, Y, Kosugi, Y, Restrepo-Coupe, N, Huete, A, Zhang, J, Liu, Y-H, Zhang, X, Liu, W-J, Zhao, J-F, Zeng, J, Song, Q-H, Chen, Y-J, Song, L & Tan, Z-H 2023, 'Asian tropical forests assimilating carbon under dry conditions: water stress or light benefits?', Journal of Plant Ecology, vol. 16, no. 3.
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AbstractTropical forests are characterized by vast biomass, complex structures and mega-biodiversity. However, the adaptation processes of these forests to seasonal water availability are less understood, especially those located in the monsoonal and mountainous regions of tropical Southeast Asia. This study used four representative tropical forests spanning from 2° N to 22° N in continental Southeast Asia to address dry-condition photosynthesis at the seasonal scale. We first provided novel and reliable estimations of ecosystem photosynthesis (gross primary production; GPP) seasonality at all four sites. As expected, both evergreen and deciduous seasonal forests exhibited higher GPPs during the rainy season than during the dry season. A bimodal pattern corresponding to solar radiation occurred in the GPP of the perhumid forest. The surface conductance (Gs) was consistently lower both in the dry season and during dry spells (DSPs) than during the wet season and non-dry spells. However, this did not prevent GPP from increasing alongside increasing irradiance in the perhumid forest, suggesting that other ecosystem physiological properties, for example, the light-saturated photosynthetic rate, must have increased, thus surpassing the effect of Gs reduction. Thus, perhumid forests could be defined as light-demanding ecosystems with regard to their seasonal dynamics. Seasonal forests are water-stressed ecosystems in the dry season, as shown by the reductions in GPP, Gs and related ecosystem physiological properties. At all four forest sites, we observed a lack of consistent adaptive strategy to fit the water seasonality due to the diversity in leaf phenology, soil nutrient availability, root depth and other potential factors.

Yang, X, Liang, B, Xue, D, Liang, J, Zaslawski, C & Chen, J 2023, 'Global research trends in acupuncture for cancer pain: A bibliometric analysis', Medicine, vol. 102, no. 41, pp. e34739-e34739.
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Background: In recent years, acupuncture has gained popularity in the management of cancer-related pain (CRP). This study aims to use bibliometric analysis to investigate the historical development, recent hotspots and research trends in this field. Methods: The Web of Science Core Collection database was selected as the data source for this study to retrieve and obtain literature related to acupuncture and CRP. Data analyses were performed with CiteSpace and VOSviewer to conduct the bibliometric analysis. Results: This bibliometric analysis was conducted from 2000 to 2022. A total of 664 publications were included in this work. The number of publications has steadily increased over the last 2 decades. The United States has the largest number of published articles (244 papers), while the People’s Republic of China has the highest centrality (0.48). The primary research institutions were Memorial Sloan-Kettering Cancer Center, Kyung Hee University and Beijing University of Chinese Medicine. Mao Jun J. was the most prolific author, while Heather Greenlee was the most cited one. The most productive journal was Integrative Cancer Therapies. The most frequent keywords excluding the search subject were “electroacupuncture,” “management,” “quality of life,” “breast cancer,” “Aromatase inhibitor,” “neuropathic pain,” “mechanisms,” and “protocol.” Conclusion: This study explored the application value of acupuncture in the management of CRP with bibliometric analysis, offering an intuitive understanding of this topic and revealing the hotspots and research trends. ...

Yang, X, Zhang, B, Tian, Y, Wang, Y, Fu, Z, Zhou, D, Liu, H, Kang, F, Li, B, Wang, C & Wang, G 2023, 'Electrolyte design principles for developing quasi-solid-state rechargeable halide-ion batteries', Nature Communications, vol. 14, no. 1, p. 925.
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AbstractRechargeable halide-ion batteries (HIBs) are good candidates for large-scale due to their appealing energy density, low cost, and dendrite-free features. However, state-of-the-art electrolytes limit the HIBs’ performance and cycle life. Here, via experimental measurements and modelling approach, we demonstrate that the dissolutions in the electrolyte of transition metal and elemental halogen from the positive electrode and discharge products from the negative electrode cause the HIBs failure. To circumvent these issues, we propose the combination of fluorinated low-polarity solvents with a gelation treatment to prevent dissolutions at the interphase, thus, improving the HIBs’ performance. Using this approach, we develop a quasi-solid-state Cl-ion-conducting gel polymer electrolyte. This electrolyte is tested in a single-layer pouch cell configuration with an iron oxychloride-based positive electrode and a lithium metal negative electrode at 25 °C and 125 mA g–1. The pouch delivers an initial discharge capacity of 210 mAh g–1and a discharge capacity retention of almost 80% after 100 cycles. We also report assembly and testing of fluoride-ion and bromide-ion cells using quasi-solid-state halide-ion-conducting gel polymer electrolyte.

York, E, McNaughton, DA, Duman, M-N, Gale, PA & Rawling, T 2023, 'Fatty Acid-Activated Proton Transport by Bisaryl Anion Transporters Depolarises Mitochondria and Reduces the Viability of MDA-MB-231 Breast Cancer Cells', Biomolecules, vol. 13, no. 8, pp. 1202-1202.
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In respiring mitochondria, the proton gradient across the inner mitochondrial membrane is used to drive ATP production. Mitochondrial uncouplers, which are typically weak acid protonophores, can disrupt this process to induce mitochondrial dysfunction and apoptosis in cancer cells. We have shown that bisaryl urea-based anion transporters can also mediate mitochondrial uncoupling through a novel fatty acid-activated proton transport mechanism, where the bisaryl urea promotes the transbilayer movement of deprotonated fatty acids and proton transport. In this paper, we investigated the impact of replacing the urea group with squaramide, amide and diurea anion binding motifs. Bisaryl squaramides were found to depolarise mitochondria and reduce MDA-MB-231 breast cancer cell viability to similar extents as their urea counterpart. Bisaryl amides and diureas were less active and required higher concentrations to produce these effects. For all scaffolds, the substitution of the bisaryl rings with lipophilic electron-withdrawing groups was required for activity. An investigation of the proton transport mechanism in vesicles showed that active compounds participate in fatty acid-activated proton transport, except for a squaramide analogue, which was sufficiently acidic to act as a classical protonophore and transport protons in the absence of free fatty acids.

Zavafer, A, Bates, H, Mancilla, C & Ralph, PJ 2023, 'Phenomics: conceptualization and importance for plant physiology', Trends in Plant Science, vol. 28, no. 9, pp. 1004-1013.
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Zavan, L, Fang, H, Johnston, EL, Whitchurch, C, Greening, DW, Hill, AF & Kaparakis‐Liaskos, M 2023, 'The mechanism of Pseudomonas aeruginosa outer membrane vesicle biogenesis determines their protein composition', PROTEOMICS, vol. 23, no. 10, pp. 2200464-2200464.
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AbstractGram‐negative bacteria produce outer membrane vesicles (OMVs) and contain bacterial cargo including nucleic acids and proteins. The proteome of OMVs can be altered by various factors including bacterial growth stage, growth conditions, and environmental factors. However, it is currently unknown if the mechanism of OMV biogenesis can determine their proteome. In this study, we examined whether the mechanisms of OMV biogenesis influenced the production and protein composition of Pseudomonas aeruginosa OMVs. OMVs were isolated from three P. aeruginosa strains that produced OMVs either by budding alone, by explosive cell lysis, or by both budding and explosive cell lysis. We identified that the mechanism of OMV biogenesis dictated OMV quantity. Furthermore, a global proteomic analysis comparing the proteome of OMVs to their parent bacteria showed significant differences in the identification of proteins in bacteria and OMVs. Finally, we determined that the mechanism of OMV biogenesis influenced the protein composition of OMVs, as OMVs released by distinct mechanisms of biogenesis differed significantly from one another in their proteome and functional enrichment analysis. Overall, our findings reveal that the mechanism of OMV biogenesis is a main factor that determines the OMV proteome which may affect their subsequent biological functions.

Zhand, S, Zhu, Y, Nazari, H, Sadraeian, M, Warkiani, ME & Jin, D 2023, 'Correction to “Thiolate DNAzymes on Gold Nanoparticles for Isothermal Amplification and Detection of Mesothelioma-derived Exosomal PD-L1 mRNA”', Analytical Chemistry, vol. 95, no. 32, pp. 12193-12193.
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Zhand, S, Zhu, Y, Nazari, H, Sadraeian, M, Warkiani, ME & Jin, D 2023, 'Thiolate DNAzymes on Gold Nanoparticles for Isothermal Amplification and Detection of Mesothelioma-derived Exosomal PD-L1 mRNA', Analytical Chemistry, vol. 95, no. 6, pp. 3228-3237.
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Catalytic DNAzymes have been used for isothermal amplification and rapid detection of nucleic acids, holding the potential for point-of-care testing applications. However, when Subzymes (universal substrate and DNAzyme) are tethered to the polystyrene magnetic microparticles via biotin-streptavidin bonds, the residual free Subzymes are often detached from the microparticle surface, which causes a significant degree of false positives. Here, we attached dithiol-modified Subzyme to gold nanoparticle and improved the limit of detection (LoD) by 200 times compared to that using magnetic microparticles. As a proof of concept, we applied our new method for the detection of exosomal programed cell-death ligand 1 (PD-L1) RNA. As the classical immune checkpoint, molecule PD-L1, found in small extracellular vesicles (sEVs, traditionally called exosomes), can reflect the antitumor immune response for predicting immunotherapy response. We achieved the LoD as low as 50 fM in detecting both the RNA homologous to the PD-L1 gene and exosomal PD-L1 RNAs extracted from epithelioid and nonepithelioid subtypes of mesothelioma cell lines, which only takes 8 min of reaction time. As the first application of isothermal DNAzymes for detecting exosomal PD-L1 RNA, this work suggests new point-of-care testing potentials toward clinical translations.

Zhang, C, Feng, J, Guo, X, Zhang, J, Zhang, W, Zhang, L, Song, J, Shao, G & Wang, G 2023, 'Blocking polysulfide by physical confinement and catalytic conversion of SiO2@MXene for Li–S battery', Applied Physics Letters, vol. 122, no. 19.
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Lithium–sulfur (Li–S) batteries have attracted increasing attention for next-generation energy storage systems with a high energy density and low cost. However, the practical applications have been plagued by the sluggish reaction kinetics and the shuttle effect of lithium polysulfides (LiPSs). Herein, core–shell SiO2@Ti3C2Tx MXene (SiO2@MX) hollow spheres are constructed as multifunctional catalysts to boost the performance of Li–S batteries. The dual-polar and dual-physical properties of SiO2 core and MXene shell provide multiple defense lines to the shuttle effect by chemical and physical confinement to LiPSs. Density functional theory calculations prove that Ti3C2Tx MXene and SiO2 enable the stronger trapping ability of LiPSs and the fast Li2S decomposition process. With this strategy, the robust SiO2@MX/S electrodes deliver superior electrochemical performances, including a high capacity of 1263 mAh g−1, and remarkable cycling stability with an ultralow capacity decay of 0.04% per cycle over 1000 cycles at 1 C. This work highlights the significance of core-shell dual-polar structural sulfur catalysts for practical application in advanced Li–S batteries.

Zhang, H, Chen, Y, Hua, W, Gu, W, Zhuang, H, Li, H, Jiang, X, Mao, Y, Liu, Y, Jin, D & Bu, W 2023, 'Heterostructures with Built‐in Electric Fields for Long‐lasting Chemodynamic Therapy', Angewandte Chemie International Edition, vol. 62, no. 15.
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AbstractSustained signal activation by hydroxyl radicals (⋅OH) has great significance, especially for tumor treatment, but remains challenging. Here, a built‐in electric field (BIEF)‐driven strategy was proposed for sustainable generation of ⋅OH, thereby achieving long‐lasting chemodynamic therapy (LCDT). As a proof of concept, a novel Janus‐like Fe@Fe3O4−Cu2O heterogeneous catalyst was designed and synthesized, in which the BIEF induced the transfer of electrons in the Fe core to the surface, reducing ≡Cu2+ to ≡Cu+, thus achieving continuous Fenton‐like reactions and ⋅OH release for over 18 h, which is approximately 12 times longer than that of Fe3O4−Cu2O and 72 times longer than that of Cu2O nanoparticles. In vitro and in vivo antitumor results indicated that sustained ⋅OH levels led to persistent extracellular regulated protein kinases (ERK) signal activation and irreparable oxidative damage to tumor cells, which promoted irreversible tumor apoptosis. Importantly, this strategy provides ideas for developing long‐acting nanoplatforms for various applications.

Zhang, H, Chen, Y, Hua, W, Gu, W, Zhuang, H, Li, H, Jiang, X, Mao, Y, Liu, Y, Jin, D & Bu, W 2023, 'Heterostructures with Built‐in Electric Fields for Long‐lasting Chemodynamic Therapy', Angewandte Chemie, vol. 135, no. 15.
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AbstractSustained signal activation by hydroxyl radicals (⋅OH) has great significance, especially for tumor treatment, but remains challenging. Here, a built‐in electric field (BIEF)‐driven strategy was proposed for sustainable generation of ⋅OH, thereby achieving long‐lasting chemodynamic therapy (LCDT). As a proof of concept, a novel Janus‐like Fe@Fe3O4−Cu2O heterogeneous catalyst was designed and synthesized, in which the BIEF induced the transfer of electrons in the Fe core to the surface, reducing ≡Cu2+ to ≡Cu+, thus achieving continuous Fenton‐like reactions and ⋅OH release for over 18 h, which is approximately 12 times longer than that of Fe3O4−Cu2O and 72 times longer than that of Cu2O nanoparticles. In vitro and in vivo antitumor results indicated that sustained ⋅OH levels led to persistent extracellular regulated protein kinases (ERK) signal activation and irreparable oxidative damage to tumor cells, which promoted irreversible tumor apoptosis. Importantly, this strategy provides ideas for developing long‐acting nanoplatforms for various applications.

Zhang, L & Jin, D 2023, 'Cytometry and analytical methods in COVID‐19 diagnostics and potential treatment: A special issue on Cytometry Part A', Cytometry Part A, vol. 103, no. 2, pp. 105-106.
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Zhang, L, Cao, C, Tay, SS, Chen, C, Macmillan, A, Wen, S, Jin, D, McCarroll, J & Stenzel, MH 2023, 'Exploring the Effect of Drug Loading on the Biological Fate of Polymer-Coated Solid Nanoparticles', Chemistry of Materials, vol. 35, no. 11, pp. 4471-4488.
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Zhang, Z, Cescatti, A, Wang, Y-P, Gentine, P, Xiao, J, Guanter, L, Huete, AR, Wu, J, Chen, JM, Ju, W, Peñuelas, J & Zhang, Y 2023, 'Large diurnal compensatory effects mitigate the response of Amazonian forests to atmospheric warming and drying', Science Advances, vol. 9, no. 21, p. eabq4974.
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Photosynthesis and evapotranspiration in Amazonian forests are major contributors to the global carbon and water cycles. However, their diurnal patterns and responses to atmospheric warming and drying at regional scale remain unclear, hindering the understanding of global carbon and water cycles. Here, we used proxies of photosynthesis and evapotranspiration from the International Space Station to reveal a strong depression of dry season afternoon photosynthesis (by 6.7 ± 2.4%) and evapotranspiration (by 6.1 ± 3.1%). Photosynthesis positively responds to vapor pressure deficit (VPD) in the morning, but negatively in the afternoon. Furthermore, we projected that the regionally depressed afternoon photosynthesis will be compensated by their increases in the morning in future dry seasons. These results shed new light on the complex interplay of climate with carbon and water fluxes in Amazonian forests and provide evidence on the emerging environmental constraints of primary productivity that may improve the robustness of future projections.

Zhao, Y, Shen, Z, Huo, J, Cao, X, Ou, P, Qu, J, Nie, X, Zhang, J, Wu, M, Wang, G & Liu, H 2023, 'Epoxy‐rich Fe Single Atom Sites Boost Oxygen Reduction Electrocatalysis', Angewandte Chemie International Edition, vol. 62, no. 36.
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AbstractElectrocatalysts for highly efficient oxygen reduction reaction (ORR) are crucial for energy conversion and storage devices. Single‐atom catalysts with maximized metal utilization and altered electronic structure are the most promising alternatives to replace current benchmark precious metals. However, the atomic level understanding of the functional role for each species at the anchoring sites is still unclear and poorly elucidated. Herein, we report Fe single atom catalysts with the sulfur and oxygen functional groups near the atomically dispersed metal centers (Fe1/NSOC) for highly efficient ORR. The Fe1/NSOC delivers a half‐wave potential of 0.92 V vs. RHE, which is much better than those of commercial Pt/C (0.88 V), Fe single atoms on N‐doped carbon (Fe1/NC, 0.89 V) and most reported nonprecious metal catalysts. The spectroscopic measurements reveal that the presence of sulfur group induces the formation of epoxy groups near the FeN4S2 centers, which not only modulate the electronic structure of Fe single atoms but also participate the catalytic process to improve the kinetics. The density functional theory calculations demonstrate the existence of sulfur and epoxy group engineer the charges of Fe reactive center and facilitate the reductive release of OH* (rate‐limiting step), thus boosting the overall oxygen reduction efficiency.

Zhao, Y, Shen, Z, Huo, J, Cao, X, Ou, P, Qu, J, Nie, X, Zhang, J, Wu, M, Wang, G & Liu, H 2023, 'Epoxy‐rich Fe Single Atom Sites Boost Oxygen Reduction Electrocatalysis', Angewandte Chemie, vol. 135, no. 36.
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AbstractElectrocatalysts for highly efficient oxygen reduction reaction (ORR) are crucial for energy conversion and storage devices. Single‐atom catalysts with maximized metal utilization and altered electronic structure are the most promising alternatives to replace current benchmark precious metals. However, the atomic level understanding of the functional role for each species at the anchoring sites is still unclear and poorly elucidated. Herein, we report Fe single atom catalysts with the sulfur and oxygen functional groups near the atomically dispersed metal centers (Fe1/NSOC) for highly efficient ORR. The Fe1/NSOC delivers a half‐wave potential of 0.92 V vs. RHE, which is much better than those of commercial Pt/C (0.88 V), Fe single atoms on N‐doped carbon (Fe1/NC, 0.89 V) and most reported nonprecious metal catalysts. The spectroscopic measurements reveal that the presence of sulfur group induces the formation of epoxy groups near the FeN4S2 centers, which not only modulate the electronic structure of Fe single atoms but also participate the catalytic process to improve the kinetics. The density functional theory calculations demonstrate the existence of sulfur and epoxy group engineer the charges of Fe reactive center and facilitate the reductive release of OH* (rate‐limiting step), thus boosting the overall oxygen reduction efficiency.

Zheng, J, Ma, F-J, Liao, C, Bing, J, Tang, S, Soufiani, AM, Lee Chin, R, Xue, C, Qu, J, Yang, L, Mahmud, MA, Sun, Z, Leung, TL, Wang, G, Cairney, JM, Bremner, S, McKenzie, DR, Huang, S & Ho-Baillie, AWY 2023, 'Efficient perovskite solar cell on steel enabled by diffusion barrier and surface passivation', Cell Reports Physical Science, vol. 4, no. 9, pp. 101543-101543.
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Zheng, L, Xiong, Y, Gao, Y, Yin, F, Szczygiełda, M, Krajewska, M, Vo, PHN, Jiang, C & Liu, H 2023, 'Tailoring the draw solution chemistry in the integrated electro-Fenton and forward osmosis for enhancing emerging contaminants removal: Performance, DFT calculation and degradation pathway', Science of The Total Environment, vol. 872, pp. 162155-162155.
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Zhigulin, I, Horder, J, Ivády, V, White, SJU, Gale, A, Li, C, Lobo, CJ, Toth, M, Aharonovich, I & Kianinia, M 2023, 'Stark Effect of Blue Quantum Emitters in Hexagonal Boron Nitride', Physical Review Applied, vol. 19, no. 4, p. 044011.
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Inhomogeneous broadening is a major limitation for the application of quantum emitters in hexagonal boron nitride to integrated quantum photonics. Here we demonstrate that so-called blue emitters with an emission wavelength of 436 nm are less sensitive to electric fields than other quantum emitters in hexagonal boron nitride. Our measurements reveal a weak, predominantly quadratic Stark effect that indicates a negligible transition dipole moment of the defect. Using these results, we discuss implications for the symmetry of the defect and use density-functional-theory simulations to identify a likely atomic structure of blue emitters in hexagonal boron nitride.

Zhigulin, I, Yamamura, K, Ivády, V, Gale, A, Horder, J, Lobo, CJ, Kianinia, M, Toth, M & Aharonovich, I 2023, 'Photophysics of blue quantum emitters in hexagonal boron nitride', Materials for Quantum Technology, vol. 3, no. 1, pp. 015002-015002.
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Abstract Colour centres in hexagonal boron nitride (hBN) have emerged as intriguing contenders for integrated quantum photonics. In this work, we present a detailed photophysical analysis of hBN single emitters emitting at the blue spectral range. The emitters are fabricated by different electron beam irradiation and annealing conditions and exhibit narrow-band luminescence centred at 436 nm. Photon statistics as well as rigorous photodynamics analysis unveils potential level structure of the emitters, which suggests lack of a metastable state, supported by a theoretical analysis. The potential defect can have an electronic structure with fully occupied defect state in the lower half of the hBN band gap and empty defect state in the upper half of the band gap. Overall, our results are important to understand the photophysical properties of the emerging family of blue quantum emitters in hBN as potential sources for scalable quantum photonic applications.

Zhou, X, Liu, H, Liu, S, zhang, L, Wang, T, Wang, C & Su, D 2023, 'Constructing efficient ɑ-Fe2O3/g-C3N4/HNTs-loaded heterojunction photocatalysts for photocatalytic oxidative desulfurization: Influencing factors, kinetics, and mechanism', Fuel, vol. 332, pp. 126147-126147.
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The ɑ-Fe2O3/g-C3N4/HNTs (halloysite nanotubes) were prepared by a simple two-step calcination method. The HNTs skeleton increases the specific surface area of the material and enriches the adsorption reaction sites to prevent the reunion of g-C3N4, while ɑ-Fe2O3 further enhances the absorption in the visible region of g-C3N4. The transfer and separation of photogenerated carriers are promoted by the heterojunction structure constructed by ɑ-Fe2O3 and g-C3N4. The results showed that dibenzothiophene in model oil could be converted by 96.01 % in 3 h under visible light irradiation using ɑ-Fe2O3/g-C3N4/HNTs-10 as the photocatalyst. The electron paramagnetic resonance spectrometry, radical capture experiments, and gas chromatography-mass spectrometry indicated that hydroxyl radicals, holes, and superoxide radicals were the main active substances of the photocatalytic system. Based on the above experimental analysis, the photocatalytic desulfurization mechanism of ɑ-Fe2O3/g-C3N4/HNTs composites was proposed. This work opens a new path for the development of novel and advanced clay-based photocatalytic materials.

Zhu, Y, Luo, X, Yu, Z, Wen, S, Bao, G, Zhang, L, Zhang, C & Xian, Y 2023, 'Dye-sensitized rare-earth-doped nanoprobe for simultaneously enhanced NIR-II imaging and precise treatment of bacterial infection', Acta Biomaterialia, vol. 170, pp. 532-542.
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Zhu, Y, Zhu, R, Guan, P, Li, M, Wan, T, Hu, L, Zhang, S, Liu, C, Su, D, Liu, Y, Liu, D, Li, Q, Yu, J & Chu, D 2023, 'Designing MXene-Wrapped AgCl@Carbon core shell cathode for robust quasi-solid-state Ag-Zn battery with ultralong cycle life', Energy Storage Materials, vol. 60, pp. 102836-102836.
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Zong, L, Yu, Y, Wang, J, Liu, P, Feng, W, Dai, X, Chen, L, Gunawan, C, Jimmy Yun, SL, Amal, R, Cheong, S, Gu, Z & Chen, Y 2023, 'Oxygen-vacancy-rich molybdenum carbide MXene nanonetworks for ultrasound-triggered and capturing-enhanced sonocatalytic bacteria eradication', Biomaterials, vol. 296, pp. 122074-122074.
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Incurable bacterial infection and intractable multidrug resistance remain critical challenges in public health. A prevalent approach against bacterial infection is phototherapy including photothermal and photodynamic therapy, which is unfortunately limited by low penetration depth of light accompanied with inevitable hyperthermia and phototoxicity damaging healthy tissues. Thus, eco-friendly strategy with biocompatibility and high antimicrobial efficacy against bacteria is urgently desired. Herein, we propose and develop an oxygen-vacancy-rich MoOxin situ on fluorine-free Mo2C MXene with unique neural-network-like structure, namely MoOx@Mo2C nanonetworks, in which their desirable antibacterial effectiveness originates from bacteria-capturing ability and robust reactive oxygen species (ROS) generation under precise ultrasound (US) irradiation. The high-performance, broad-spectrum microbicidal activity of MoOx@Mo2C nanonetworks without damaging normal tissues is validated based on systematic in vitro and in vivo assessments. Additionally, RNA sequencing analysis illuminates that the underlying bactericidal mechanism is attributed to the chaotic homeostasis and disruptive peptide metabolisms on bacteria instigated by MoOx@Mo2C nanonetworks under US stimulation. Considering antibacterial efficiency and a high degree of biosafety, we envision that the MoOx@Mo2C nanonetworks can serve as a distinct antimicrobial nanosystem to fight against diverse pathogenic bacteria, especially eradicating multidrug-resistant bacteria-induced deep tissue infection.

Zou, F, Liu, Y, Chen, Z, Zhanghao, K & Jin, D 2023, 'Fourier Channel Attention Powered Lightweight Network for Image Segmentation', IEEE Journal of Translational Engineering in Health and Medicine, vol. 11, pp. 252-260.
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Adil, M, Mahmud, MAP, Kouzani, AZ & Khoo, SY 1970, 'Optimal Energy Trade in Retailer, Charging Station, and Electric Vehicles using a Stackelberg Game', 2023 IEEE IAS Global Conference on Renewable Energy and Hydrogen Technologies (GlobConHT), 2023 IEEE IAS Global Conference on Renewable Energy and Hydrogen Technologies (GlobConHT), IEEE.
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Atieh, A, Nanda, P & Mohanty, M 1970, 'A Zero-Trust Framework for Industrial Internet of Things', 2023 International Conference on Computing, Networking and Communications (ICNC), 2023 International Conference on Computing, Networking and Communications (ICNC), IEEE.
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Awatade, N, Budden, K, Nichol, K, Veerati, P, Reid, A, Hansbro, P & Wark, P 1970, 'Altered epithelial ion transport and ciliary functions in COPD', RESPIROLOGY, WILEY, pp. 74-74.

Barnes, J, Plank, M, Asquith, K, Maltby, S, Rodrigues, SL, Kaiko, G, Lochrin, A, Horvat, J, Mayall, J, Kim, R, Hansbro, P, Keely, S, Belz, G, Tay, H & Foster, P 1970, 'T-helper-22 cells develop independently of Th17 cells during bacterial infection', RESPIROLOGY, WILEY, pp. 40-40.

Bracke, KR, Jacobs, M, Anckaert, J, Faiz, A, Van Gaever, F, Verschraegen, S, Salhi, B, Schynkel, T, Venken, K, Elewaut, D, Hansbro, P, Brusselle, GG, Mestdagh, P & Seys, LJM 1970, 'Crosstalk Between Memory B Cells and Fibroblasts Contributes to COPD Pathogenesis', C108. IMMUNITY AND INFLAMMATION IN COPD: NOVEL FINDINGS, American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC, American Thoracic Society, pp. a6151-a6151.
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Carroll, O, Brown, A, Mayall, J, Gomez, H, Kim, R, Donovan, C, Williams, E, Berthon, B, Pinkerton, J, Hansbro, P, Foster, P, Wynne, K, Scott, H, Wood, L & Horvat, J 1970, 'A relationship between female sex hormones, cellular metabolism, and asthma', RESPIROLOGY, WILEY, pp. 5-5.

Chen, X, Ye, X, Mohanty, M & Manoharan, S 1970, 'Detecting Offensive Posts on Social Media', 2023 International Conference on Electrical, Computer and Energy Technologies (ICECET), 2023 International Conference on Electrical, Computer and Energy Technologies (ICECET), IEEE.
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Daly, K, Hsu, A, Nichol, K, Mayall, J, Horvat, J, Hansbro, P & Wark, P 1970, 'Recombinant Histone Deacetylase 6 (rHDAC6) treatment protects against influenza A virus (IAV) infection and disease in vivo', 10.01 - Respiratory infections and bronchiectasis, ERS Lung Science Conference 2023 abstracts, European Respiratory Society.
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Faiz, A, Pouwels, SD, Guryev, V, Boedijono, FS, Kerstjens, H, Klooster, K, Hartman, JE, Timens, W, Brandsma, C-A, Slebos, D-J & Berge, MVD 1970, 'Exome seq of patients with severe COPD and advanced emphysema', Molecular pathology and functional genomics, ERS International Congress 2023 abstracts, European Respiratory Society.
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Faiz, A, Wang, Y, da Silva, SBC, Ly, N, Leijs, A, Ninaber, D, van Hemert, M, Hiemstra, P & van der Does, A 1970, 'RNA-sequencing unravels unique host-response to infection with SARS-CoV-2', RESPIROLOGY, WILEY, pp. 106-106.

Horder, J, White, SJU, Gale, A, Li, C, Watanabe, K, Taniguchi, T, Kianinia, M, Aharonovich, I & Toth, M 1970, 'Resonant Spectroscopy of Blue Quantum Emitters in Hexagonal Boron Nitride', CLEO 2023, CLEO: Fundamental Science, Optica Publishing Group.
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A site-specific fabrication technique was used to produce arrays of blue quantum emitters in hBN for a cryogenic spectroscopy study. We characterise temperature dependent linewidth, identify processes that limit emitter coherence, and observe Rabi oscillations.

Horvat, J, Vanka, K, Kim, R, Brown, A, Donovan, C, Ali, M, Gomez, H, Palanisami, T, James, C, Williams, K, Ilic, D & Hansbro, P 1970, 'Investigating the effects of occupational dust exposures on respiratory health', RESPIROLOGY, WILEY, pp. 60-60.

Irga, P, Sharman, L, Rojahn, J, Wooster, E, Torpy, F & Fleck, R 1970, 'Green Roof and Photovoltaik comparative research in Sydney', Weltkongress Gebaudegrun / World Green Infrastructure Congress WGIC, Berlin, Germany.

Jacobs, M, Anckaert, J, Faiz, A, Van Gaever, F, Verschraegen, S, Salhi, B, Schynkel, T, Venken, K, Elewaut, D, Hansbro, P, Brusselle, G, Mestdagh, P, Seys, L & Bracke, K 1970, 'Crosstalk between memory B cells and fibroblasts contributes to COPD pathogenesis', Airway cell biology and immunopathology, ERS International Congress 2023 abstracts, European Respiratory Society.
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Jena, R, Singh, P & Mohanty, M 1970, 'PPAuth: A Privacy-Preserving Framework for Authentication of Digital Image', Springer Nature Switzerland, pp. 188-199.
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Jing, Z, Suleiman, B, Yaqub, W & Mohanty, M 1970, 'Dissemination of Fact-Checked News Does Not Combat False News: Empirical Analysis', Springer Nature Singapore, pp. 122-133.
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Johansen, M, Idrees, S, Boedijono, F, Miemczyk, S, Nguyen, D, Nichol, K, Wark, P, Faiz, A & Hansbro, P 1970, 'Late Breaking Abstract - Increased SARS-CoV-2 infection in asthmatic primary bronchial epithelial cells defined with single cell RNA-sequencing', Respiratory infections and bronchiectasis, ERS International Congress 2023 abstracts, European Respiratory Society.
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Karp, T, Faiz, A, Kerstjens, HAM, Nawijn, MC, Sun, Y, Kersten, ETG, Koppelman, GH, Kraft, M, Beghé, B, Rabe, KF, Kotz, M, Papi, A, Brightling, CE, Singh, D, Van Der Molen, T, Siddiqui, S, Guryev, V & Van Den Berge, M 1970, 'Late Breaking Abstract - Seasonal variation in nasal epithelium gene expression', Monitoring airway disease, ERS International Congress 2023 abstracts, European Respiratory Society.
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Mahbub, R, Brandsma, C, van den Berge, M & Faiz, A 1970, 'Unique COPD signatures relate to the severity of the disease', RESPIROLOGY, WILEY, pp. 42-42.

Mahbub, RM, Brandsma, C-A, Van Den Berge, M & Faiz, A 1970, 'Uncovering unique gene signatures for COPD through integrating human airway datasets', Molecular pathology and functional genomics, ERS International Congress 2023 abstracts, European Respiratory Society.
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Mahmodi, H, Bradbury, P, Cidem, A, Ong, HX, Traini, D & Kabakova, IV 1970, 'Spatial reorganization of F-actin in respiratory cells as measured by Brillouin microscopy', Emerging Technologies for Cell and Tissue Characterization II, Emerging Technologies for Cell and Tissue Characterization, SPIE.
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Martin, L, Thomas, P, De Silva, P & Sirivivatnanon, V 1970, 'Durability Loss in Concrete Due to ASR-DEF, The Role of Aggregate Reactivity in Deleterious Delayed Ettringite Formation', Concrete 2023 Resilient and Sustainable Concrete: Breaking Down Barriers, Concrete Institute of Australia Biennial National Conference, Perth.
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Durability of concrete and cementitious materials is important to their worldwide usage in housing and infrastructure. Two known causes of durability loss in concrete are the alkali-silica reaction (ASR) and delayed ettringite formation (DEF), which are chemical processes with the potential for expansion, cracking, and strength loss in affected elements. There is significant overlap in the contributing factors for ASR and DEF, in particular pore solution alkalinity. DEF is of most concern for large, precast concrete structures, although in Australia reported cases of deleterious DEF have been in conjunction with mild or moderate ASR. Current guidelines regarding DEF are based on laboratory experiments in mortar specimens, and the role of the aggregate and ASR in concrete has been overlooked. Mitigation strategies for DEF involve temperature thresholds during curing, chemical limits for the binder, and the use of supplementary cementitious materials (SCMs) in the mix design. This study investigates the role of aggregate reactivity, curing temperature, and cement composition in the susceptibility of concrete elements to deleterious DEF, and the efficacy of fly-ash as an SCM in preventing deleterious ASR-DEF. Concrete specimens containing ASR-reactive aggregates were made with different binder and curing conditions, then monitored for expansion and strength loss over two years. Contributions towards the understanding of ASR-DEF mechanisms and the development of industry risk assessments in Australia are presented in this paper.

Martin, L, Thomas, P, De Silva, P & Sirivivatnanon, V 1970, 'Role of Aggregate Reactivity, Binder Composition, and Curing Temperature on the Delayed Ettringite Formation and Associated Durability Loss in Concrete', Springer Nature Singapore, pp. 83-91.
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AbstractThe durability of concrete is critical to its worldwide use as a structural material for buildings and infrastructure, with the lifetime service of concrete greatly affecting its economic, environmental, and social costs. Causes of durability loss in some concrete structures can be attributed to the alkali–silica reaction (ASR) and delayed ettringite formation (DEF). Both are chemical reactions that have the potential to cause expansion and strength loss in affected elements. Significant overlap exists in the factors contributing to ASR and DEF in concrete structures, with widely reported evidence of deleterious DEF frequently occurring in conjunction with mild or moderate ASR. For precast concrete, experiments in mortars have provided limits in the alkali and sulfate content of the binder and maximum curing temperatures used to minimize DEF risk. The role of other constituents in concrete specimens, notably the aggregate, has been overlooked. We investigated the role of reactive aggregates and ASR in the susceptibility of concrete to deleterious DEF.

Martins, CGG, Karmaus, W, Murphy, V, Gibson, P, Hansbro, P, Starkey, M, Taylor, S, Rogers, G, Mattes, J & Collison, A 1970, 'Cord blood pDCs are associated with microbiome at 6 weeks', RESPIROLOGY, WILEY, pp. 134-134.

Mayall, J, Cooper, G, Donovan, C, Haw, T, Budden, K, Blomme, E, Maes, T, Kong, C, Horvat, J, Khakoo, S, Wilkinson, T, Hansbro, P & Staples, K 1970, 'Anti-viral responses of tissue-resident NK cells are dysregulated in COPD', RESPIROLOGY, WILEY, pp. 42-42.

Mayall, J, Pillar, A, Daly, K, Brown, A, Essilfie, A, Gomez, H, Kim, R, Nichol, K, Donovan, C, Anderson, G, Frazer, D, Milward, E, Hansbro, P, Reid, D, Hsu, A, Wark, P & Horvat, J 1970, 'Iron metabolism determines the outcome of influenza A virus infection', 10.01 - Respiratory infections and bronchiectasis, ERS Lung Science Conference 2023 abstracts, European Respiratory Society.
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Mayall, J, Pillar, A, Daly, K, Brown, A, Essilfie, A-T, Gomez, H, Kim, R, Nichol, K, Donovan, C, Anderson, G, Frazer, D, Milward, E, Hansbro, P, Reid, D, Hsu, A, Wark, P & Horvat, J 1970, 'LSC - 2023 - Iron metabolism determines the outcome of influenza A virus infection', Respiratory infections and bronchiectasis, ERS International Congress 2023 abstracts, European Respiratory Society.
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McDonald, V, Archbold, G, Beyene, T, Brew, B, Franklin, P, Gibson, P, Harrington, J, Hansbro, P, Johnston, F, Robinson, P, Sutherland, M, Yates, D, Zosky, G & Abramson, M 1970, 'Landscape fire smoke and asthma: A proposed TSANZ position statement', RESPIROLOGY, WILEY, pp. 111-112.

Merklein, M, Goulden, L, Kiewiet, M, Liu, Y, Lai, CK, Choi, D-Y, Madden, SJ, Poulton, CG & Eggleton, BJ 1970, 'Temporal Dynamics of On-Chip Quasi-Light Storage', 2023 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC), 2023 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference (CLEO/Europe-EQEC), IEEE.
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Nouman, M, Sara, H, Khoo, SY, Mahmud, MAP & Kouzani, AZ 1970, 'Mental Health Prediction through Text Chat Conversations', 2023 International Joint Conference on Neural Networks (IJCNN), 2023 International Joint Conference on Neural Networks (IJCNN), IEEE.
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Parker, H, Jahan, Z, Oliver, BGG, Faiz, A, Cheung, V, Cooper, WA & Kohonen-Corish, MRJ 1970, 'Defining tetranucleotide repeat instability as a marker of deficient DNA repair in lung cancer', RESPIROLOGY, WILEY, pp. 41-41.

Rahman, H, Nanda, P, Mohanty, M & Sheikh, N 1970, 'Anomaly Detection in Smart Grid Networks Using Power Consumption Data', Proceedings of the 20th International Conference on Security and Cryptography, 20th International Conference on Security and Cryptography, SCITEPRESS - Science and Technology Publications, Rome, Italy.
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Rathnayake, MS, Willemse, B, Vermeulen, C, Hacken, N, Timens, W, Kooistra, W, Heijink, I, Oliver, B, Berge, M & Faiz, A 1970, 'Longitudinal effects of one-year smoking-cessation on human bronchial-epithelial cell composition', RESPIROLOGY, WILEY, pp. 137-137.

Rathnayake, S, Reddy, K, Xenaki, D, Oliver, B, Van Den Berge, M & Faiz, A 1970, 'The ALDH3A1 gene suppresses Periostin gene expression in human airway epithelial cells exposed to cigarette smoke', Mechanisms of lung injury and repair, ERS International Congress 2023 abstracts, European Respiratory Society.
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Reddy, K, Xenaki, D, Rathanyake, S, Idrees, S, Boedijono, F, Weckmann, M, Padula, M, Van Den Berge, M, Faiz, A & Oliver, B 1970, 'The X and Y of inflammation, fibrosis and cell death in asthma', Molecular pathology and functional genomics, ERS International Congress 2023 abstracts, European Respiratory Society.
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Reddy, KD, Xenaki, D, Rathnayake, S, Zakarya, R, Idrees, S, Boedijono, F, Padula, M, Van Den Berge, M, Faiz, A & Oliver, B 1970, 'Cigarette smoking, COPD and the sex chromosomes', Molecular pathology and functional genomics, ERS International Congress 2023 abstracts, European Respiratory Society.
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Rehman, S, Budden, K, Quaranta, A, Fuchs, D, Bowerman, K, Vaughan, A, Shukla, S, Brown, A, Alemao, C, Balachandra, L, Gomez, H, Kumar, V, Idrees, S, Faiz, A, Hugenholtz, P, Wark, P, Horvat, J, Wood, L, Wheelock, C & Hansbro, P 1970, 'Role of dietary lipids in chronic obstructive pulmonary disease', RESPIROLOGY, WILEY, pp. 154-154.

Saerens, G, Dursap, T, Solntsev, AS, Karvounis, A, Hesner, I, Duong, NMH, Regreny, P, Maeder, A, Morandi, A, Danescu, A, Chauvin, N, Chapman, RJ, Penuelas, J & Grange, R 1970, 'Single GaAs Nanowires for Near-Infrared Spontaneous Parametric Down-Conversion', CLEO 2023, CLEO: Fundamental Science, Optica Publishing Group.
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We report 60 GHz/Wm photon pair generation via type-0 spontaneous parametric down-conversion at 1550 nm from individual free-standing GaAs nanowires with sub-450 nm diameter and lengths up to 5 μm.

Sarma, A, Faiz, A, Ditz, B, Langelier, C, Nerella, S, Neff, N, Lyden, A, Caldera, S, Bolourchi, S, Calfee, CS, Bathoorn, E, Kerstjens, HAM, Van den Berge, M & Christenson, S 1970, 'Unsupervised Clustering of Sputum Transcriptomes Identifies Three COPD Exacerbation Endotypes With Differing Susceptibilities and Pathobiology', B101. OMICS STUDIES OF IMMUNE CELLS AND THE LUNG, American Thoracic Society 2023 International Conference, May 19-24, 2023 - Washington, DC, American Thoracic Society.
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Tu, J, Li, W, Hansbro, P, Das, A, Yang, C, Zou, J & Diwan, A 1970, 'Smoking and Tetramer Tryptase Accelerate Intervertebral Disc Degeneration by Inducing METTL14-Mediated DIXDC1 m6 Modification', MOLECULAR THERAPY, CELL PRESS, pp. 332-332.

van Nijnatten, J, Faiz, A, Timens, W, Guryev, V, Slebos, D, Klooster, K, Hartman, J, Kole, T, Choy, D, Grimbaldeston, M, Rosenberger, C, Partners, G, Heijink, I, Pouwels, S, Kerstjens, H, Brandsma, C & van den Berge, M 1970, 'A gene-signature for severe-COPD with accordance in the upper/lower airways', RESPIROLOGY, WILEY, pp. 92-92.

van Nijnatten, J, Faiz, A, Vermeulen, CJ, Timens, W, De Vries, M, Faner, R, Brandsma, C-A & Van Den Berge, M 1970, 'Differential DNA Methylation Associated with COPD and COPD Severity', Molecular pathology and functional genomics, ERS International Congress 2023 abstracts, European Respiratory Society.
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Wadhwa, R, Kim, R, Jayaraman, R, Nguyen D, H, Donovan, C, Galvao, I, Johansen, M, Gillis, C, Philip, A, Khan, H, Hansbro, N, Adcock, I, Wark, P, O'Neill, L, Dua, K & Hansbro, P 1970, 'The mitochondrial metabolite itaconate suppresses the pathogenesis of experimental COPD', RESPIROLOGY, WILEY, pp. 156-157.

Wajahat, M, Kouzani, AZ, Khoo, SY & Mahmud, MAP 1970, 'Development of Triboelectric Nanogenerator Using Flexible 3D Printed Polyamide', 2023 IEEE International Flexible Electronics Technology Conference (IFETC), 2023 IEEE International Flexible Electronics Technology Conference (IFETC), IEEE.
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White, S, Yang, T, Dontschuk, N, Stewart, C, Li, C, Xu, Z-Q, Solntsev, AS, Kianinia, M, Stacey, A, Toth, M & Aharonovich, I 1970, 'Hexagonal boron nitride: a source for quantum photonics applications', Light-Emitting Devices, Materials, and Applications XXVII, Light-Emitting Devices, Materials, and Applications XXVII, SPIE.
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Yaqub, W, Mohanty, M & Suleiman, B 1970, 'Proctoring Online Exam Using Eye Tracking', Proceedings of the 20th International Conference on Security and Cryptography, 20th International Conference on Security and Cryptography, SCITEPRESS - Science and Technology Publications.
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Ajani, P, Dove, M, Farrell, H, O'Connor, W, Tesoriero, M, Verma, A, Zammit, A, Hughes, B & Murray, S University of Technology Sydney 2023, Transforming Australian Shellfish Production: Cromartys Bay Harvest Area, Port Stephens. Report on Stage 1, December 2017-March 2021, Sydney, Australia, Sydney Australia.

Ajani, P, Dove, M, Farrell, H, O'Connor, W, Tesoriero, M, Verma, A, Zammit, A, Hughes, B & Murray, S University of Technology Sydney 2023, Transforming Australian Shellfish Production: Wapengo Front Lake Harvest Area, Wapengo Lake. Report on Stage 1, December 2018-March 2021, Sydney.

Ajani, P, Dove, M, Farrell, H, O'Connor, W, Tesoriero, M, Verma, A, Zammit, A, Hughes, B & Murray, S University of Technology Sydney 2023, Transforming Australian Shellfish Production: Wonboyn Lake A Harvest Area, Wonboyn River. Report on Stage 1, February 2018-February 2021, Sydney, Australia, Sydney, Australia.

Ajani, P, Dove, M, Farrell, H, O'Connor, W, Tesoriero, M, Verma, A, Zammit, A, Hughes, B, Parker, L & Murray, S University of Technology Sydney 2023, Transforming Australian Shellfish Production: Gogleys Lagoon Harvest Area, Camden Haven River. Report on Stage 1, October 2017-March 2021, Sydney.

Ajani, P, Vig, D, Dove, M, Farrell, H, O'Connor, W, Tesoriero, M, Verma, A, Zammit, A, Hughes, B & Murray, S University of Technology Sydney 2023, Transforming Australian Shellfish Production: Quibray Bay Harvest Area, Georges River. Report on Stage 1, October 2017-March 2021, Sydney, Australia.

Abell-King, C, Pokhrel, A, Rice, SA, Duggin, IG & Söderström, B 2023, 'Bacterial multispecies invasion of human epithelial bladder cells', Cold Spring Harbor Laboratory.
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Afrose, D, Nikolic, V, Orlic, N, Mikovic, Z, Stefanovic, M, Cakic, Z, Hansbro, P, Su, P & McClements, L 2023, 'Uric acid is a promising biomarker and target of preeclampsia', Elsevier BV, pp. e50-e50.
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Alamil, JMR, Xenaki, D, Manandhar, B, Paudel, KR, Hansbro, PM, Oliver, BG, Chellappan, DK & Dua, K 2023, 'Agarwood oil nanoemulsion attenuates production of lipopolysaccharide (LPS)-induced proinflammatory cytokines, IL-6 and IL-8 in human bronchial epithelial cells.', IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund, pp. 681-685.
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Awatade, NT, Reid, AT, Nichol, KS, Budden, KF, Veerati, PC, Pathinayake, PS, Grainge, CL, Hansbro, PM & Wark, PAB 2023, 'Comparison of Commercially Available Differentiation Media on Cell Morphology, Function, and Anti-Viral Responses in Conditionally Reprogrammed Human Bronchial Epithelial Cells', Research Square Platform LLC.
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Awatade, NT, Reid, AT, Nichol, KS, Budden, KF, Veerati, PC, Pathinayake, PS, Grainge, CL, Hansbro, PM & Wark, PAB 2023, 'Comparison of commercially available differentiation media on morphology, function, and virus-host interaction in conditionally reprogrammed human bronchial epithelial cells', Cold Spring Harbor Laboratory.
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Borra, A, Valova, V, Fleming, C, Irga, P, Torpy, F, Gunaway, C, Cole, L & McGrath, K 2023, 'Air Pollutant Particles and Their Effects on the Heart', Elsevier BV, pp. S407-S407.
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Bottomley, A, Motha, A, Kruik, S & Cole, L 2023, 'Research Data Management in a Core Imaging Facility: Common challenges and best practice'.

Bozier, J, Wang, B, de Vries, M, Brandsma, C-A, van den Berge, M, Timens, W, Heijink, IH, Oliver, BGG & Woldhuis, RR 2023, 'E-cigarette vapour induces cellular senescence in primary lung fibroblasts and may contribute to lung pathology', Cold Spring Harbor Laboratory.
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Briceño, VF, Cook, AM, Courtney Jones, SK, Arnold, PA, Gallagher, RV, French, K, Bravo, LA, Nicotra, AB & Leigh, A 2023, 'Drivers of thermal tolerance breadth of plants across contrasting biomes: do mean or seasonality in climate indices matter more?', Cold Spring Harbor Laboratory.
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Brunet, M, Duff, NL, Rigaut-Jalabert, F, Romac, S, Barbeyron, T & Thomas, F 2023, 'Seasonal dynamics of a glycan-degrading flavobacterial genus in a tidally-mixed coastal temperate habitat', Cold Spring Harbor Laboratory.
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Budden, K, Awatade, N, Gallop, M, Paudel, K, Nichol, K, Hegarty, K, Hansbro, P & Wark, P 2023, 'Bushfire-derived particulates impair epithelial cilia and CFTR chloride channel functions'.

Budden, KF, Shukla, SD, Bowerman, KL, Gellatly, S, Wood, DLA, Lachner, N, Idrees, S, Patel, VK, Faiz, A, Rehman, SF, Donovan, C, Alemao, CA, Shen, SJ, Vanka, KS, Mason, J, Haw, TJ, Fricker, M, Keely, S, Hansbro, NG, Belz, GT, Horvat, JC, Ashhurst, TM, van Vreden, C, McGuire, HM, de St Groth, BF, King, NJC, Crossett, B, Cordwel, SJ, Bonaguro, L, Schultze, JL, Forster, SC, Cooper, MA, Segal, LN, Vaughan, A, Collins, PF, Bowman, RV, Fong, KM, Yang, IA, Wark, PA, Dennis, PG, Hugenholtz, P & Hansbro, PM 2023, 'Fecal microbial transfer and complex carbohydrates mediate protection against COPD', Cold Spring Harbor Laboratory.
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Cai, Y, Shang, Y, Qin, X, Jin, D & zhou, J 2023, 'Anisotropic surface quenching of upconversion nanoparticles', Research Square Platform LLC.
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Carter, DJ, Byrne, MK, Djordjevic, S, Robertson, H, Labbate, M, Morgan, B & Billington, L 2023, 'Antimicrobial Resistance Surveillance Technology: Keys to Success', Center for Open Science.
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Carter, DJ, Byrne, MK, Djordjevic, S, Robertson, H, Labbate, M, Morgan, B & Billington, L 2023, 'Public Support for Next-Generation Antimicrobial Resistance Surveillance', Center for Open Science.
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Cook, A, Rezende, E, Petrou, K & Leigh, A 2023, 'Beyond a single temperature threshold: applying a cumulative thermal stress framework to plant heat tolerance', Authorea, Inc..
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Cortesi, M, Liu, D, Yee, C, Marsh, DJ & Ford, CE 2023, 'Model Parameter identification using 2D vs 3D experimental data: a comparative analysis', Cold Spring Harbor Laboratory.
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de Almeida Oliveira, M, Lopes Amorim, N, Torres, L, Prazeres, PHDM, Junior, REM, Vaughan, A, Wadhwa, R, Majumder, R, Das, S, Paudel, KR, Evans, A, Moreira, TG, Maioli, TU, Hansbro, P & Faria, AMC 2023, 'Omega 3 anti-inflammatory effects are microbiota dependent: unravelling the gut-lung axis'.

De Rubis, G, Paudel, KR & Dua, K 2023, 'Modernizing traditional medicine: nanoparticle-based drug delivery systems to improve the delivery of phytoceuticals in managing chronic respiratory diseases'.

De Rubis, G, Paudel, KR, Liu, G, Hansbro, P, Adams, J, Oliver, B & Dua, K 2023, 'Berberine-loaded nanoparticles attenuate TGF-β-induced remodelling features in human bronchial epithelial cells'.

Elwakil, BH, Hamed, MT & Paudel, KR 2023, 'Recent insights of fucoidan probiotic and its effect on gut microbiota.', IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund, pp. 556-558.
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Espinoza-Vergara, G, Hoque, MM, Noorian, P, To, J, Moon, JM, Rice, SA & McDougald, D 2023, 'Single cell RNA-seq reveals that the Vibrio cholerae MakA toxin is required for killing of Tetrahymena pyriformis and for survival in protozoan expelled food vacuoles', Research Square Platform LLC.
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Faiz, A, Mahbub, R, Sabrina Boedijono, F, Timens, W, Nawijn, MC, Hansbro, P, D. Johansen, M, Brandsma, C-A, Heijink, IH, Massip, F, Stella de Biase, M, F. Schwarz, R, Adcock, IM, Chung, KF, Hiemstra, PS, Goulaouic, H, Heming Xing, H, Abdulai, RM, de Rinaldis, E, Cunoosamy, D, Harel, S, Lederer, DJ, C Nivens, M, Kerstjens, HAM, Hylkema, M & Van den Berge, M 2023, 'Using Single Cell Sequencing to Understand Treatment Response to Anti-IL33 Treatment in Chronic Obstructive Pulmonary Disease (COPD)', American Thoracic Society.
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Gale, A, Scognamiglio, D, Zhigulin, I, Whitefield, B, Kianinia, M, Aharonovich, I & Toth, M 2023, 'Manipulating the Charge State of Spin Defects in Hexagonal Boron Nitride'.

George, AM 2023, 'ABC Transporters 45 Years On', MDPI AG, pp. 16789-16789.
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ABC transporters constitute one of the largest gene families among all species [...]

Ghaly, TM, Focardi, A, Elbourne, LDH, Sutcliffe, B, Humphreys, W, Paulsen, IT & Tetu, SG 2023, 'Stratified microbial communities in Australia’s only anchialine cave are taxonomically novel and drive chemotrophic energy production via coupled nitrogen-sulphur cycling', Cold Spring Harbor Laboratory.
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Ghorbanpour, S, Richards, C, Cole, L, McGrath, K, Warkiani, ME & McClements, L 2023, 'New 3D multicellular models of placental tissue for studying important mechanisms of preeclampsia', Elsevier BV, pp. e6-e6.
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Ghorbanpour, S, Richards, C, Pienaar, D, Sesperez, K, Aboulkheyr Es, H, Nikolic, V, Karadzov-Orlic, N, Mikovic, Z, Stefanovic, M, Cakic, Z, Alqudah, A, Cole, L, Gorrie, C, Mcgrath, K, Kavurma, MM, Warkiani, ME & McClements, L 2023, 'SC3_3. FKBPL signalling in placental development and preeclampsia', Elsevier BV, pp. e77-e78.
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Gillette, GM, Camp, EF, Edmondson, J, Booth, DJ, Scott, RI & Suggett, DJ 2023, 'Fish-based herbivory and the natural maintenance of algal fouling on coral nurseries used across the Great Barrier Reef', Research Square Platform LLC.
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Gupta, A 2023, 'Why Western Sydney is feeling the heat from climate change more than the rest of the city', The Conversation.
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https://theconversation.com/why-western-sydney-is-feeling-the-heat-from-climate-change-more-than-the-rest-of-the-city-201477

Hamm, JN, Liao, Y, Kügelgen, AV, Dombrowski, N, Landers, E, Brownlee, C, Johansson, EMV, Whan, RM, Baker, MAB, Baum, B, Bharat, TAM, Duggin, IG, Spang, A & Cavicchioli, R 2023, 'The parasitic lifestyle of an archaeal symbiont', Cold Spring Harbor Laboratory.
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Hennessey, M, Whitefield, B, Gale, A, Scott, JA, Kianinia, M, Aharonovich, I & Toth, M 2023, 'Framework for engineering of spin defects in hexagonal boron nitride by focused ion beams'.

Hossain, MS, Bacaoco, M, Mai, TNA, Ponchon, G, Chen, C, Ding, L, Chen, Y, Ekimov, E, Xu, H, Solntsev, AS & Tran, TT 2023, 'Fiber-based Ratiometric Optical Thermometry with Silicon-Vacancy in Microdiamonds'.

Idrees, S, Pathinayake, P, Faiz, A, Wark, P & Hansbro, P 2023, 'Identification of genes and master regulators driving COPD progression'.

Idrees, S, Pathinayake, P, Faiz, A, Wark, P & Hansbro, P 2023, 'Identification of new target genes in COPD'.

Jha, BK, Imran, M, Mohammed, Y, Jha, LA, Paudel, KR & Jha, SK 2023, 'Progress on Understanding Metabolic Syndrome, and Knowledge of Its Complex Pathophysiology', MDPI AG.
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Jha, SK, Kumar, B, Paudel, KR & Bandyopadhyay, A 2023, 'The application of bioglass to treat osteoarthritis.', EXCLI JOURNAL MANAGING OFFICE, pp. 1232-1234.
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Jin, D, Mi, C, Zhang, X, Yang, C, Wu, J, Chen, X, Ma, C, Wu, S, Yang, Z, Qiao, P, Liu, Y, Wu, W, Guo, Z, Liao, J, zhou, J, Guan, M, Liang, C & Liu, C 2023, 'Bone Disease Imaging through the Near-Infrared-II Window', Research Square Platform LLC.
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JOSHUA, S, NASSIF, NT & SIMPSON, AM 2023, '903-P: Correlation of Gene Expression and Cellular Pathways in Insulin-Expressing Mouse Liver Cells Transduced with an Integrating Adeno-associated Viral Vector (AAV)', American Diabetes Association.
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Gene therapy is being considered as a treatment/cure for type 1 diabetes (T1D). Previously we used a clinically-applicable AAV to deliver furin cleavable insulin (INS-FUR) to the livers of diabetic non-obese diabetic mice. The traditional AAV8 that allows predominantly episomal expression, and the hybrid AAV8/piggyBac that results in transgene integration into the host genome were used. Euglycaemia was achieved in mice (n=4) that received AAV8/piggyBac-INS-FUR, but not in mice that received AAV8-INS-FUR. In the current study global transcriptomic profiling was carried out, by total RNA sequencing, to compare the key pathways modulated in hepatocytes that reversed diabetes with those that did not. Using Qiagen CLC Workbench, significant genes were identified based on fold change expression cut offs of, and a false discovery rate p-value of &lt;0.05. Selected genes were mapped onto the various cellular pathways using Qiagen Ingenuity Pathway Analysis (IPA) software to determine trends in pathway activation/ inactivation related to the altered gene expression. IPA analysis showed that the canonical pathways identified between the treatments remained largely the same, however their downstream biological processes differed. Key canonical pathways identified include pathways related to insulin signalling, glucose and lipid metabolism. Key pathway players identified as significantly altered in the comparative treatments included insulin, major histocompatibility complex class I, A, glucose-6-phosphatase catalytic subunit 1 and insulin like growth factor binding protein 1. The profile of AAV8/piggyBac-INS-FUR transduced mouse livers resembled that of a normal liver compared to livers transduced with AAV8-INS-FUR. This study confirms the correlation of transcriptomic data mapping and has identified differences in the cellular effects of both vector systems used to deliver INS-FUR for T1D treatment. ...

Kalam, SN, Dowland, S, Cole, L, Lindsay, L & Murphy, CR 2023, 'Extracellular vesicles, syntaxin 2 and SNAP23 collectively play a role in the receptive uterine microenvironment', Cold Spring Harbor Laboratory.
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Katona, K, Sklibosios Nikitopoulos, C & Schlögl, E 2023, 'A Price Mechanism Survey of the Australian National Electricity Market', SSRN.

Kaur, J, Gulati, M, Pandey, NK, Khatik, GL, Sudhakar, S, Alotaibi, F, Kumar, D, Shukla, MK, Kumar, P, Famta, P, Arora, P, Okaiyeto, K, Oguntibeju, OO, Gupta, G, Paudel, KR, Dua, K & Singh, SK 2023, 'Antidiabetic evaluation of vanillic acid-glyburide loaded polymeric micelles in high fat diet and streptozotocin induced diabetic rats', Research Square Platform LLC.
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Lam, MMC & Hamidian, M 2023, 'Examining the role ofAcinetobacter baumanniiPlasmid Types in Disseminating Antimicrobial Resistance', Cold Spring Harbor Laboratory.
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Lendo, CIN, Camp, EF, Edmondson, J, Hughes, DJ, Kuzhiumparambil, U, Clases, D, de Vega, RG & Suggett, DJ 2023, 'Multiple trait approach to inform ecosystem service value of corals propagated for restoration on the Great Barrier Reef', Research Square Platform LLC.
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Li, W, Lin, A, Hutton, M, Dhaliwal, H, Nadel, J, Rodor, J, Tumanov, S, Örd, T, Hadden, M, Mokry, M, Mol, BM, Pasterkamp, G, Padula, MP, Geczy, CL, Ramaswamy, Y, Sluimer, JC, Kaikkonen, MU, Stocker, R, Baker, AH, Fisher, EA, Patel, S & Misra, A 2023, 'Colchicine promotes atherosclerotic plaque stability independently of inflammation', Cold Spring Harbor Laboratory.
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Mao, H, Szafranska, K, Kruse, L, Holte, C, Wolfson, DL, Ahluwalia, BS, Whitchurch, CB, Cole, L, Lockwood, GP, Diekmann, R, Le Couteur, D, Cogger, VC & McCourt, PAG 2023, 'Effect of caffeine and other xanthines on liver sinusoidal endothelial cell ultrastructure', Cold Spring Harbor Laboratory.
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Martino, DJ, Bui, DS, Li, S, Idrose, S, Perret, J, Lowe, AJ, Lodge, CJ, Bowatte, G, Moodley, Y, Thomas, PS, Zosky, G, Hansbro, PM, Holloway, JW, Svanes, C, Faner, R, Walters, EH & Dharmage, SC 2023, 'Genetic and Epigenetic Associations with Pre–Chronic Obstructive Pulmonary Disease Lung Function Trajectories', American Thoracic Society, pp. 1135-1137.
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McClements, L, Ghorbanpour, S, Cartland, S, Seth, S, Ecker, R, Richards, C, McGrath, K, Cole, L, Warkiani, M & Kavurma, M 2023, 'FK506-Binding Protein Like (FKBPL) Regulates Hypoxia-induced Factor-α and Restores Endothelial Function and Vascular Integrity in Ischaemia-induced Angiogenesis', Elsevier BV, pp. S412-S412.
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McEntee, CP, Houston, S, Finlay, CM, Rossi, S, Liu, G, Shaw, TN, Casulli, J, Fife, M, Smedley, C, Griffith, TS, Pepper, M, Hussell, T, Hansbro, PM, Schwartz, J-M, Paidassi, H & Travis, MA 2023, 'A subset of CD4+ effector memory T cells limit immunity to pulmonary viral infection and prevent tissue pathology via activation of latent TGFβ', Cold Spring Harbor Laboratory.
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McKnight, DJE, Wong, J, Okoh, EB, Snijders, F, Lidbetter, F, Webster, J, Haughton, M, Darling, AE, Djordjevic, SP, Bogema, DR & Chapman, T 2023, 'Xanthomonas rydalmerenesissp. nov., a novel plant bacteria isolated fromFragaria x ananassa', Cold Spring Harbor Laboratory.
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Mediati, DG, Dan, W, Lalaouna, D, Dinh, H, Pokhrel, A, Stinear, TP, Cain, AK & Tree, JJ 2023, 'The 3’ UTR ofvigRis required for virulence inStaphylococcus aureusand has expanded through STAR sequence repeat insertions', Cold Spring Harbor Laboratory.
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Menictas, M, Oates, CJ & Wand, MP 2023, 'Real-time Semiparametric Regression via Sequential Monte Carlo'.

Mi, C, Zhang, X, Yang, C, Wu, J, Chen, X, Ma, C, Wu, S, Yang, Z, Qiao, P, Liu, Y, Wu, W, Guo, Z, Liao, J, Zhou, J, Guan, M, Liang, C, Liu, C & Jin, D 2023, 'Nanoparticles Passive Targeting Allows Optical Imaging of Bone Diseases'.

Miller, SM, Herdean, A, Gupta, V, Signal, B, Abbriano, RM, Ralph, PJ & Pernice, M 2023, 'FACS-mediated selection enhances growth and carotenoid production in subpopulations of Phaeodactylum tricornutum', Research Square Platform LLC.
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Mills, J, Gebhard, LJ, Schubotz, F, Shevchenko, A, Speth, DR, Liao, Y, Duggin, IG, Marchfelder, A & Erdmann, S 2023, 'Extracellular vesicles of Euryarchaeida: precursor to eukaryotic membrane trafficking', Cold Spring Harbor Laboratory.
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Mishra, N, Bhatt, S, Paudel, KR, Hansbro, P & Dua, K 2023, 'Synbiotics for the management of Cancer', Springer.
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This book illustrates the significance of probiotics and prebiotics for the management of various types of cancers.

Mohamad, MSB, Reyes, R-J, De Rubis, G, Paudel, KR, Hansbro, PM, Dua, K & Chellappan, DK 2023, 'The versatility of 18ß-glycyrrhetinic acid in attenuating pulmonary inflammatory disorders.', pp. 188-190.
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Narang, P, Haghi, M, Burke, C & Oliver, B 2023, 'Human Upper Respiratory Tract Microbiome and Epithelium Interactions', European Respiratory Society.
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Nomura, H, Wu, M, Song, J, Hung, A, Tran, S, TA, H, Akther, F, Wu, Y, Johansen, M, Chew, K, Kumar, V, Woodruff, T, Clark, R, Koehbach, J, Lomonte, B, Rosado, C, Thomas, M, Boudes, M, Reboul, C, Rash, L, Gallo, L, Essid, S, Elmlund, D, Miemczyk, S, Hansbro, N, Saunders, B, Britton, W, Sly, P, Yamamoto, A, Fernández, J, Moyle, P, Short, K, Hansbro, P, Kuruppu, S, Smith, I & Rajapakse, N 2023, 'Development of a novel angiotensin converting enzyme 2 stimulator with broad implications in SARS-CoV2 infection and type 1 diabetes', Research Square Platform LLC.
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Nonahal, M, Li, C, Ren, H, Spencer, L, Kianinia, M, Toth, M & Aharonovich, I 2023, 'Monolithic Platform for Integrated Quantum Photonics with Hexagonal Boron Nitride'.

Paudel, KR 2023, 'Impact of bushfire smoke particulate matter exposure on respiratory health.'.
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Invited speaker at TSANZ Symposium - Breathing in vitro - Exposure of in vitro models to aerosolsMonday, 27 March 202315:30 - 17:00

Paudel, KR, Manandhar, B, Singh, SK, Gupta, G, Hansbro, PM, Chellappan, DK & Dua, K 2023, 'Cytotoxic mechanisms of berberine-phytantriol liquid crystalline nanoparticles against non-small-cell lung cancer.', IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund, pp. 516-519.
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Phan, TH, Shi, H, Denes, CE, Cole, AJ, Wang, Y, Cheng, YY, Hesselson, D, Neely, GG, Jang, J-H & Chrzanowski, W 2023, 'Advanced pathophysiology mimicking lung models for accelerated drug discovery', Research Square Platform LLC.
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Pinagé, ER, Bell, DM, Longo, M, Silva, CA, Csillik, O & Huete, AR 2023, 'Surface energy dynamics and canopy structural properties in intact and disturbed forests in the Southern Amazon', Authorea, Inc..
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Platen, E 2023, 'Entropy-Maximizing Dynamics of Continuous Markets'.

Rehman, SF, Fuchs, D, Budden, KF, Quaranta, A, Shukla, SD, Horvat, J, Wood, LG, Wheelock, CE & Hansbro, PM 2023, 'Lipid Profiling Reveals Key Lipid Mediators in Cigarette Smoke-induced Experimental COPD', American Thoracic Society, pp. a6148-a6148.
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Ren, B, He, H, Cao, M, Gao, Y, Zheng, P, Yan, S, Zhong, J-H, Wang, L & Jin, D 2023, 'Noise Learning of Instruments for High-contrast, High-resolution and Fast Hyperspectral Microscopy and Nanoscopy', Research Square Platform LLC.
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Rennie, C, Sives, C, Boyton, I, Diaz, D, Gorrie, CA, Vittorio, O, Collins-Praino, L & Care, A 2023, 'In vivofate of systemically administered encapsulin protein nanocages and implications for their use in targeted drug delivery', Cold Spring Harbor Laboratory.
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Robertson, IO, Scholten, SC, Singh, P, Healey, AJ, Meneses, F, Reineck, P, Abe, H, Ohshima, T, Kianinia, M, Aharonovich, I & Tetienne, J-P 2023, 'Detection of paramagnetic spins with an ultrathin van der Waals quantum sensor'.

Ryan, TAJ, Hooftman, A, Rehill, AM, Johansen, MD, O’ Brien, EC, Toller-Kawahisa, JE, Wilk, MM, Day, EA, Weiss, HJ, Sarvari, P, Vozza, EG, Schramm, F, Peace, CG, Zotta, A, Miemczyk, S, Nalkurthi, C, Hansbro, NG, McManus, G, O’Doherty, L, Gargan, S, Long, A, Dunne, J, Cheallaigh, CN, Conlon, N, Carty, M, Fallon, PG, Mills, KHG, Creagh, EM, O’ Donnell, JS, Hertzog, PJ, Hansbro, PM, McLoughlin, RM, Wygrecka, M, Preston, RJS, Zasłona, Z & O’Neill, LAJ 2023, 'Publisher Correction: Dimethyl fumarate and 4-octyl itaconate are anticoagulants that suppress Tissue Factor in macrophages via inhibition of Type I Interferon', Springer Science and Business Media LLC, p. 4374.
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The original version of this Article contained an error in the spelling of the surname for the author Luke A J O’Neill, which was incorrectly given as ‘O’ Neill’ with an additional space. This has now been corrected in both the PDF and HTML versions of the Article.

Sadaf, T, Chung, F, Neely, G, Faiz, A & Hansbro, P 2023, 'Genome-wide CRISPR-Cas9 knock-out library screening against cigarette smoke'.

Sadaf, T, Paudel, KR, Gillis, C, Nijnatten, JV, Kim, R, Beckett, EL, Deane, A, Faiz, A & Hansbro, P 2023, 'Integration of miRNA and gene expression profiles from lung tissues of CS-induced COPD'.

Scammell, H & Sushkov, O 2023, 'Exciton condensation in biased bilayer graphene'.
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Scholten, SC, Singh, P, Healey, AJ, Robertson, IO, Haim, G, Tan, C, Broadway, DA, Wang, L, Abe, H, Ohshima, T, Kianinia, M, Reineck, P, Aharonovich, I & Tetienne, J-P 2023, 'Multi-species optically addressable spin defects in a van der Waals material'.

Shrestha, J, Paudel, KR, Nazari, H, Dharwal, V, Bazaz, SR, Johansen, MD, Dua, K, Hansbro, PM & Warkiani, ME 2023, 'Front Cover Image, Volume 43, Issue 5', Wiley, pp. i-i.
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Sortino, L, Gale, A, Kühner, L, Li, C, Biechteler, J, Wendisch, FJ, Kianinia, M, Ren, H, Toth, M, Maier, SA, Aharonovich, I & Tittl, A 2023, 'Optically addressable spin defects coupled to bound states in the continuum metasurfaces'.

Strudwick, P, Camp, EF, Seymour, J, Roper, C, Edmondson, J, Howlett, L & Suggett, DJ 2023, 'Assessing Efficacy of Plastic-free Alternative Ties For Coral Propagation in Reef Restoration', Research Square Platform LLC.
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Strudwick, P, Seymour, J, Camp, E, Roper, C, Edmondson, J, Howlett, L & Suggett, D 2023, 'Bacterial communities associated with corals out-planted on the Great Barrier Reef are inherently dynamic over space and time', Research Square Platform LLC.
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Stylianou, N, Sebina, I, Matigian, N, Monkman, J, Doehler, H, Röhl, J, Allenby, M, Nam, A, Pan, L, Rockstroh, A, Sadeghirad, H, Chung, K, Sobanski, T, O’Byrne, K, Ana Clara Simoes, FA, Rebutini, PZ, Machado-Souza, C, Stonoga, ETS, Warkiani, ME, Salomon, C, Short, K, McClements, L, de Noronha, L, Huang, R, Belz, GT, Souza-Fonseca-Guimaraes, F, Clifton, V & Kulasinghe, A 2023, 'Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies placental dysfunction signatures', Cold Spring Harbor Laboratory.
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Tang, S-J, Zhang, M, Sun, J, Meng, J-W, Xiong, X, Gong, Q, Jin, D, Yang, Q-F & Xiao, Y-F 2023, 'Single-particle vibrational spectroscopy using optical microresonators'.

Tobin, L, Jarocki, VM, Kenyon, J, Drigo, B, Donner, E, Djordjevic, SP & Hamidian, M 2023, 'Genomic Analysis of Diverse EnvironmentalAcinetobacterIsolates Identifies Plasmids, Antibiotic Resistance Genes, and Capsular Polysaccharides Shared with Clinical Strains', Cold Spring Harbor Laboratory.
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Tran, TN, Gale, A, Whitefield, B, Toth, M, Aharonovich, I & Kianinia, M 2023, 'Coupling spin defects in hexagonal boron nitride to a microwave cavity'.

Valova, V, Gorrie, C, McGrath, K, Borra, A, Sanchez, L & Cole, L 2023, 'Establishing a Tissue Clearing Pipeline at the Microbial Imaging Facility, UTS'.
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Optical tissue clearing techniques can improve the permeability of biological specimens to light and molecular probes, and thereby make them amenable to in toto imaging at cellular resolution. Recent advances in these techniques have demonstrated their utility for a range of specimens with different chemical and physical compositions, and enabled advances in fields such as neuroscience, developmental biology, immunology, and oncology. To facilitate access to these techniques, a tissue clearing pipeline was established at the Microbial Imaging Facility (MIF) at UTS. Three case studies are presented to highlight the challenges associated with designing clearing experiments for distinct sample types and research applications, including (1) visualising astrocytes in rat brain and spinal cord; (2) assessing VCAM-1 (inflammatory marker) expression in the mouse heart; and (3) examining the 3D structure and composition of breast cancer tumour and mammary gland pieces. In each case, a different clearing approach was adapted to suit a range of interacting variables, for example, improving sample transparency; maintaining tissue integrity; preserving molecules of interest and antigenicity; and ensuring compatibility with available imaging systems and computing resources. The need to tailor clearing pipelines to specific samples and research applications can limit the practicality of offering tissue clearing as a service in a Core Facility. However, as demonstrated by the current case studies, having capacity to offer expertise and access to a subset of protocols can help increase uptake of these techniques and enable users to progress their research on cleared specimens.

van der Ploeg, EA, Faiz, A, Teitsma, G, Melgert, BN, Horvatovich, P, Burgess, JK & Gan, T 2023, '(1226) Serum Proteomics for Fibrotic Markers in Early Detection of Bronchiolitis Obliterans Syndrome after Lung Transplantation', Elsevier BV, pp. S524-S524.
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Vlaanderen, EJ, Ghaly, TM, Moore, LR, Focardi, A, Paulsen, IT & Tetu, SG 2023, 'Plastic Leachate Exposure Drives Antibiotic Resistance and Virulence in Marine Bacterial Communities', Cold Spring Harbor Laboratory.
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Wenk, EH, Sauquet, H, Gallagher, RV, Brownlee, R, Boettiger, C, Coleman, D, Yang, S, Auld, T, Barrett, R, Brodribb, T, Choat, B, Dun, L, Ellsworth, D, Gosper, C, Guja, L, Jordan, GJ, Breton, TL, Leigh, A, Lu-Irving, P, Medlyn, B, Nolan, R, Ooi, M, Sommerville, KD, Vesk, P, White, M, Wright, IJ & Falster, DS 2023, 'The AusTraits Plant Dictionary', Cold Spring Harbor Laboratory.
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Westlund, E, Bergenstråle, A, Pokhrel, A, Chan, H, Skoglund, U, Daley, DO & Söderström, B 2023, 'Application of nanotags and nanobodies for live cell single-molecule imaging of the Z-ring inEscherichia coli', Cold Spring Harbor Laboratory.
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Wong-Brown, MWY, Johnson, Z, Salem, S, Matthews, BG, Ford, CE, Marsh, DJ & Bowden, NA 2023, 'Abstract C041: Drug repurposing to target TGF-β in chemoresistant high-grade serous ovarian cancer', American Association for Cancer Research (AACR), pp. C041-C041.
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Abstract High-grade serous ovarian cancer (HGSOC) has low 5-year survival rate of 48%, due to chemotherapy resistance. Effective new therapies are required to improve the survival rate of HGSOC. TGF-β is a family of proteins associated with epithelial-mesenchymal transition and have been implicated in ovarian cancer progression and chemoresistance. Drugs that target TGF-β may have potential to be used to treat chemoresistant HGSOC and control tumour growth and progression. Drug repurposing is a strategy to identify new uses for approved drugs outside of their original indication, and ensure timely access to efficacious and cost-effective therapy for chemoresistant HGSOC. The aims of the study is to determine the effect of the repurposed drug teniposide on HGSOC cell growth, death, and apoptosis. A ligand-based screening was performed by Cresset Discovery for approved drugs that bind to the TGF-β receptor complex and ligand. Teniposide was shortlisted according to its dosing, lipid solubility, pharmacokinetics, and side effects. MTT assays were performed on eight molecularly-characterised HGSOC cell lines to obtain the IC50 of teniposide. The effect of the IC50 dose of teniposide on HGSOC cell growth, death, and apoptosis were monitored on the IncuCyte live-cell imager. Western blotting was performed to determine the expression of TGF-β signalling pathway proteins after treatment with teniposide. The average IC50 of teniposide in HGSOC cell lines is 10µM, within the range of the maximum plasma concentration (61µM). HGSOC cell lines treated with 10µM teniposide showed decreased cell growth, and increased cell death and apoptosis, similar to HGSOC cell lines treated with clinically-relevant dose of carboplatin (30µM). HGSOC cell lines treated with 10µM teniposide showed significantly higher cell death and apoptosis compared to treatment with 30µM carboplatin. Our preliminary results show that teniposide signi...

Xi, P, Xu, X, Wang, W, Qiao, L, Fu, Y, Ge, X, Zhao, K, Zhanghao, K, Guan, M, Chen, X, Li, M & Jin, D 2023, 'Ultra-high spatio-temporal resolution imaging with parallel acquisition-readout structured illumination microscopy (PAR-SIM)', Research Square Platform LLC.
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Xiang, M, Jiang, Y, zhou, J, Bao, G, Luo, X, Zhang, L, Jin, D, Xian, Y & Zhang, C 2023, 'NIR Light-Controlled DNA Nanodevice for Amplified mRNA Imaging and Precise Gene Therapy', Research Square Platform LLC.
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Xirocostas, Z, Ollerton, J, Tamme, R, Peco, B, Lesieur, V, Slavich, E, Junker, R, Pärtel, M, Raghu, S, Uesugi, A, Bonser, S, Chiarenza, G, Hovenden, M & Moles, A 2023, 'The great escape: patterns of enemy release are not explained by time, space, or climate', California Digital Library (CDL).
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Zhang, Z, Ma, X, Meada, EE, Lu, L, Wang, Y, Xie, Z, Li, X, Huang, L, Zhao, Y & Huete, AR 2023, 'Decoupling of rainfall and vegetation greening in the arid Asian endorheic basins due to the irrigation intensification', Authorea, Inc..
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Zhigulin, I, Yamamura, K, Ivády, V, Gale, A, Horder, J, Lobo, CJ, Kianinia, M, Toth, M & Aharonovich, I 2023, 'Photophysics of blue quantum emitters in hexagonal Boron Nitride'.

Zhou, Y, Garces, LP, Shen, Y, Sherris, M & Ziveyi, J 2023, 'Age-Dependent Multi-Cohort Affine Mortality Model with Cohort Correlation', CEPAR Working Paper.